Having exact same problem on Jaunty with a Dell Precision M70 Laptop,
using Nvidia driver (ver 180xx).  Also running compiz desktop.

Here is my zsnes config file.

; PSR-produced config file (stock default in CAPS)

; Note, if you're worried you messed up a setting, removing the line will have
; ZSNES use the default settings for that option.
; The next time ZSNES is run, the line will reappear with the default settings.

;  ----
; -- Input --
;  ----

; For other input settings see zinput.cfg

; Enable Game-Specific Key Combos (0 = NO, 1 = Yes)
GUIComboGameSpec=0

; Enable Game-Specific Key Input (0 = NO, 1 = Yes)
GameSpecificInput=0

;  ----
; -- Options --
;  ----

; Allow MMX Support (0 = No, 1 = YES)
; Disable this only if you actually do NOT have a processor that supports MMX.
; Disabling this option will prevent you from using some of the more advanced
; video/sound filters.
AllowMMX=1

; Enable New Graphics Engine (0 = No, 1 = YES)
; Toggle off when there are graphical problems in the new graphics engine
newengen=1

; Enable Older Graphics Engine Tweak for Mode 2 (0 = NO, 1 = Yes)
; Enable this to see if it helps with rendering problems
; Only works with old graphic engine
bgfixer=0

; Snapshot Format (0 = BMP, 1 = PNG)
ScreenShotFormat=0

; Auto-Patch ROM with IPS (0 = No, 1 = YES)
AutoPatch=1

; Display ROM Info on Load (0 = No, 1 = YES)
DisplayInfo=1

; Log Info About the Last ROM Loaded to rominfo.txt (0 = No, 1 = YES)
RomInfo=1

; Enable FPS Counter when ZSNES is Started (0 = NO, 1 = Yes)
; This option is disabled when manual frameskip is in use.
FPSAtStart=0

; Display Clock (0 = NO, 1 = Yes)
TimerEnable=0

; Change Clock Mode (0 = 24 HOUR, 1 = 12 Hour)
TwelveHourClock=0

; Display Black Box Around Clock (0 = No, 1 = YES)
ClockBox=1

; Use Small Font for Messages (0 = NO, 1 = Yes)
SmallMsgText=0

; Transparent Messages - doesn't work with small font (0 = NO, 1 = Yes)
GUIEnableTransp=0

;  ----
; -- Video --
;  ----

; Video Mode [0..22]
;   0 = 256x224      R WIN     1 = 256x224      R FULL
;   2 = 512x448     DR WIN     3 = 512x448     DR FULL
;   4 = 640x480     DR FULL
;   5 = 256x224    O R WIN     6 = 512x448    ODR WIN
;   7 = 640x480    ODS FULL    8 = 640x480    ODS WIN
;   9 = 640x560    ODR WIN    10 = 768x672    ODR WIN
;  11 = 800x600    ODS FULL   12 = 800x600    ODS WIN
;  13 = 896x784    ODR WIN    14 = 1024x768   ODS FULL
;  15 = 1024x768   ODS WIN    16 = 1024x896   ODR WIN
;  17 = 1280x960   ODS FULL   18 = 1280x1024  ODS FULL
;  19 = 1600x1200  ODS FULL   20 = VARIABLE   ODR WIN
;  21 = VARIABLE   ODS WIN    22 = CUSTOM     OD  FULL
; You need to select the custom video mode and modify CustomResX/Y to properly
; use custom res support.
cvidmode=22
; Last windowed & fullscreen modes (used when alt-tabbing)
PrevWinMode=2
PrevFSMode=22

; Custom Resolution X and Y for Custom Video Modes [256x224..2048x1536]
CustomResX=1680
CustomResY=1050

; Enable Video Interpolation, Bilinear Filtering (0 = NO, 1 = Yes)
; Bilinear Filtering is compatible with all filters except NTSC.
; Bilinear Filtering replaces Interpolation and is OpenGL only.
; Video Interpolation is compatible with scanlines.
; Blends the neighboring pixels on the screen to eliminate pixelation.
antienab=0
BilinearFilter=0

; Enable NTSC Filter (0 = NO, 1 = Yes)
; Enable Blargg's wonderful NTSC filter which simulates the artifacts of an
; NTSC TV set - it is probably not a good idea to use with TV-out
; Recommended to use a minimum res of 602x448
NTSCFilter=0
; Blend Frames, Refresh Screen (0 = OFF, 1 = On)
; Blend Frames allows smoother transitions between frames for non-60Hz refresh 
rates.
; Refresh Screen allows the screen to be updated while changing the filter's 
parameters.
NTSCBlend=0
NTSCRef=0
; NTSC TV Attributes [-100..100]
NTSCHue=0
NTSCSat=0
NTSCCont=0
NTSCBright=0
NTSCSharp=0
NTSCGamma=0
NTSCRes=0
NTSCArt=0
NTSCFringe=0
NTSCBleed=0
NTSCWarp=0

; Enable Kreed's 2x Filters (0 = NONE, 1 = 2xSaI, 2 = Super Eagle, 3 = Super 
2xSaI)
; These are Kreed's various 2x filters. They do not exhibit the same level of
; blurring than interpolation/bilinear. MMX support is required.
; This is disabled when other filters are used.
En2xSaI=0

; Use HQ*x Filter (0 = NO, 1 = Yes)
; This is a filter MaxSt has created. These are very CPU intensive filters that
; do very awesome blending to remove the pixelation.
; This is disabled when other filters are used. MMX support is required.
hqFilter=1
; Set HQ*x level [2..4]
; Recommended min resolutions
; HQ2x = 512x448
; HQ3x = 768x672
; HQ4x = 1024x896
hqFilterlevel=2

; Enable Scanlines (0 = NONE, 1 = Full, 2 = 25%, 3 = 50%) - simulate TV 
scanlines
; This is compatible with interpolation.
scanlines=0

; Enable Grayscale Mode (0 = NO, 1 = Yes) - don't enable this for other than 
nostalgia
; The whole screen is displayed in monochrome color.
GrayscaleMode=0

; Enable High-Res Mode 7 (0 = NO, 1 = Yes)
; Doubles the internal resolution of the image when Mode 7 is in use
; However this disables most filters, except for interpolation.
; This is only useful in certain games and is not useful in general.
; Requires a minimum res of 512x448
Mode7HiRes16b=1

; Keep 4:3 Ratio (0 = No, 1 = YES)
; This is particularly handy for those that use laptops/LCDs+non 4:3 
resolutions.
; This can be used for Variable ODS Windowed and Custom Res OD Fullscreen.
; It is not recommended to enable this while under 298x224.
; Disable this if you want to use the non-standard ratio instead.
Keep4_3Ratio=1

; Set Gamma Level [0..15]
gammalevel=0

;  ----
; -- Sound --
;  ----

; libAO driver to use. Use zsnes --help to see valid list.
; However "auto" (to automatically pick best one), and "sdl" should
; always be available.
libAoDriver="auto"

; Disable SPC Emulation (0 = NO, 1 = Yes)
; Disabling SPC emulation can improve performance, but at the expense of
; emulation accuracy. There will be no sound output and games might crash.
SPCDisable=0

; Enable Sound Emulation (0 = Off, 1 = ON) - disable if you need the performance
; If SPC emulation is disabled, there will be no sound output.
soundon=1

; Enable Stereo Sound (0 = Off, 1 = ON) - disable if you need the performance
StereoSound=1

; Swap Left Audio Channel w/Right (0 = NO, 1 = Yes)
RevStereo=0

; Simulate Surround Sound (0 = NO, 1 = Yes)
; Enable a simulated 2 speaker surround sound effect.
; Do not enable if playing a game that has its own surround sound effects.
; Stereo Sound must be enabled for this to work.
Surround=0

; Sampling Rate: (0 = 8000Hz, 1 = 11025Hz, 2 = 22050Hz, 3 = 44100Hz,
;                            4 = 16000Hz, 5 = 32000Hz, 6 = 48000Hz)
; Using any other sound frequencies other than the default 32000Hz
; is COMPLETELY UNACCEPTABLE in use for sound bug reports.
SoundQuality=5

; Sound Volume Level [0..100]
MusicRelVol=100

; Enable Sound Interpolation (0 = None, 1 = GAUSSIAN, 2 = Cubic, 3 = 8-point)
; Sound interpolation smooths out the waveform of lower frequency sounds.
; Using any other setting other than the default Gaussian interpolation is
; COMPLETELY UNACCEPTABLE in sound bug reports.
SoundInterpType=3

; Enable Low-Pass Filter (0 = NONE, 1 = Simple, 2 = Dynamic, 3 = Hi-quality)
; A low-pass filter improves the bass in the sounds.
; This is useful if you have a Subwoofer.
LowPassFilterType=3

; Disable Echo (0 = NO, 1 = Yes)
; Disables the echo effect in the sound.
EchoDis=0

;  ----
; -- Saves --
;  ----

; Number of Rewind States [0..99]
RewindStates=8
; Delay between rewinds [1..99] - (1 = 200ms, 5 = 1s, 10 = 2s)
RewindFrames=15

; Don't Save SRAM (0 = NO, 1 = Yes)
; Only enable this if you don't want to Save SRAM at any given time.
; This option will make Update SRAM in Real-Time useless.
nosaveSRAM=0

; Update SRAM in Real-Time (0 = NO, 1 = Yes)
; This is useful if you fear something will prevent ZSNES from exiting normally.
; It is required to play games that store important values directly to SRAM.
; ZSNES normally updates SRAM on exit.
; If Don't Save SRAM is enabled, this option is useless.
SRAMSave5Sec=0

; Load SRAM w/Savestates (0 = No, 1 = YES)
; Enable this when you want to use the SRM that is stored within the savestate.
; Warning: You will overwrite the existing SRM that you are currently using.
; It is required to properly use states with games storing important values
; directly in SRM.
SRAMState=1

; Select Latest Save State Slot on Game Load (0 = NO, 1 = Yes)
; Enable this if you want to load the last saved savestate quickly
; (via the load savestate button/GUI option) after loading the game.
LatestSave=0

; Auto Increment State Slot First, then Save State (0 = NO, 1 = Yes)
; Enable this if you have a tendency in saving accidentally to an existing
; savestate.
AutoIncSaveSlot=0

; Save in 10 save block (0 = NO, 1 = Yes)
; This may be handy if you want to save within a block (0-9, 10-19, etc.)
AutoIncSaveSlotBlock=0

; Auto State Save/Load (0 = NO, 1 = Yes) - uses a special state
; Enable this if you wish a special state to be saved on a visit to the GUI.
; This state will automatically be loaded when you load a game.
AutoState=0

; Pause Emulation After Loading a Save State (0 = NO, 1 = Yes)
PauseLoad=0
; Pause Emulation After Using Rewind (0 = NO, 1 = Yes)
PauseRewind=0

;  ----
; -- Emulation --
;  ----

; Percent to Execute [50..150] - only modify if you know what you are doing
; Changing this value may help certain games run.
per2exec=100

; Disable Hacks (0 = NO, 1 = Yes)
; Set this to 1 if you want to disable game specific hacks
HacksDisable=0

; Frameskip: [0..10] (0 = AUTO, 1-10 = Manual 0-9)
frameskip=0

; Max Frameskip Allowed for Auto Frameskip [0..9]
maxskip=9

; Fastforward/Slowdown Keys Behaviour (0 = HELD, 1 = Toggle)
FastFwdToggle=0
; Fastforward/Slowdown Factors [0..28] (0 = factor 2, 28 = factor 30)
FFRatio=8
SDRatio=0

; Emulation Speed Throttle [0..58] (0 = speed/30, 29 = 1x, 58 = 30x)
; Fast-forward multiplicator is currently inaccurate
EmuSpeed=29

;  ----
; -- Paths --
;  ----
; It is suggested to go to GUI->Paths and modify the paths from there.
; ROMs directory
ROMPath="/home/vbundi/Final Fantasy 1 2 3 4 5 6 7 And Mystic Quest 
English+Emulators NES and SNES/ROMs/"
; Save states & SRAMs, snapshots, SPCs
SRAMPath=""
SnapPath=""
SPCPath=""
; BIOS/base carts (BS-X, Sufami Turbo, Same Game & SD Gundam G-Next)
BSXPath=""
STPath=""
SGPath=""
GNextPath=""
; SPC7110 graphic packs
FEOEZPath=""
SJNSPath=""
MDHPath=""
SPL4Path=""

;  ----
; -- GUI --
;  ----

; Disable GUI (0 = NO, 1 = Yes)
guioff=0

; Show All Files in 'Load Game' Menu (0 = NO, 1 = Yes)
showallext=0

; Filename Display Mode (0 = LONG FILENAME, 1 = Internal header name)
GUIloadfntype=0

; Recent games played, you shouldn't edit this manually (8.3 / Paths / LFN)
prevloadiname="Final_Fantasy_IV_(U).zip"\0"$    "\"Final_Fantasy_(U).zip"\0"\'  
  "\"Final Fantasy VII (NJ063) ("\0")\"   "
prevloaddnamel=0"!    "\"/home/vbundi/Final Fantasy 1 2 3 4 5 6 7 And Mystic 
Quest English+Emulators NES and SNES/ROMs/"\0"J$   "\"/home/vbundi/Final 
Fantasy 1 2 3 4 5 6 7 And Mystic Quest English+Emulators NES and 
SNES/ROMs/"\0"J$   "\"/home/vbundi/Final Fantasy 1 2 3 4 5 6 7 And Mystic Quest 
English+Emulators NES and SNES/ROMs/"\0"UJ   "
prevloadfnamel="Final_Fantasy_IV_(U).zip"\0"2%   "\"Final_Fantasy_(U).zip"\0"5% 
  "\"Final Fantasy VII (NJ063) (Ch) [T+Eng97%_Xaronyr_EnCardier].zip"\0"uJ   "

; Freeze Recent Games List (0 = NO, 1 = Yes)
prevlfreeze=0

; Right Mouse Click Enters/Exits GUI (0 = NO, 1 = Yes)
GUIRClick=0

; Left Handed Mouse Behavior for GUI (0 = NO SWAP, 1 = Swap)
; (swap left and right buttons)
lhguimouse=0

; Show Mouse Cursor Shadow (0 = No, 1 = YES)
; Displays a shadow under the mouse cursor.
mouseshad=1

; Wrap Mouse Cursor (0 = NO, 1 = Yes)
; If enabled, the cursor will wrap around to the other side.
; Only useful for Fullscreen modes.
mousewrap=0

; ESC to Game Menu (0 = No, 1 = YES)
; If yes, visiting the GUI will have the Game Menu automatically selected.
; It will also enable the main menu keyboard shortcuts.
esctomenu=1

; Control the GUI Using Gamepad 1 (0 = NO, 1 = Yes)
JoyPad1Move=0

; Filter GUI Display (0 = No, 1 = YES)
; If enabled, the current filter you are using will also filter the GUI.
FilteredGUI=1

; Use Custom Font (0 = NO, 1 = Yes)
; The font currently reads off a format as defined by zfile.txt
newfont=0

; Save GUI Window Positions (0 = NO, 1 = Yes)
savewinpos=0

; GUI windows X/Y coordinates - GUI setup showing windows #

;    Game          Config        Cheat      Netplay       Misc
; -------------------------------------------------------------------
;  1:Load         3:Input      7:Add Code  [Internet]   9:Misc Keys
;    Run          -------      7:Browse                10:GUI Opts
; 12:Reset       17:Devices   13:Search                15:Movie Opt
;  -------       18:Chip Cfg                           16:Key Comb.
; 14:Save State   -------                                 Save Cfg
;  2:Open State   4:Options                             -------
; 14:Pick State   5:Video                              11:About
;  -------        6:Sound
;    Quit        19:Paths
;                20:Saves
;                21:Speed

; X positions [-233..254] (windows #0 to #22)
GUIwinposx=0,6,65,33,42,5,34,6,64,8,8,33,56,64,56,5,3,28,48,6,28,53,0
; Y positions [8..221] (windows #0 to #22)
GUIwinposy=0,20,70,20,20,20,20,20,30,30,20,20,60,30,60,20,20,60,60,20,30,20,0

; GUI Background Effect
; (0 = NONE, 1 = Snow, 2 = Water A, 3 = Water B, 4 = Burn, 5 = Smoke)
GUIEffect=1

; GUI Palette Mods:
; Background RGB Tint [0..31]
GUIRAdd=15
GUIGAdd=10
GUIBAdd=31
; Titlebar RGB Tint [0..31]
GUITRAdd=0
GUITGAdd=10
GUITBAdd=31
; Windows RGB Tint [0..31]
GUIWRAdd=8
GUIWGAdd=8
GUIWBAdd=25

;  ----
; -- Cheats --
;  ----

; Autoload .CHT files (0 = NO, 1 = Yes)
; Enable the use of stored cheat files on load.
AutoLoadCht=0

; Selected Size Search (0 = 1 BYTE, 1 = 2B, 2 = 3B, 3 = 4B)
CheatSrcByteSize=0

; Selected Numerical Base (0 = DECIMAL, 1 = Hexadecimal)
CheatSrcByteBase=0

; Search Type (0 = EXACT VALUE, 1 = Comparative)
CheatSrcSearchType=0

; Add Code for Most Significant Byte Only (0 = NO, 1 = Yes)
CheatUpperByteOnly=0

;  ----
; -- Movies --
;  ----

; For other input settings see zmovie.cfg

; Display Movie Frame # During Record/Replay (0 = NO, 1 = Yes)
MovieDisplayFrame=0

; Movie Default Start Method (0 = NOW, 1 = Power-On,
;                             2 = Reset, 3 = Power-On without SRAM)
MovieStartMethod=0

; Switch Modes when Loading a Movie State (0 = NO, 1 = Switch to Record, 2 = 
Switch to Playback)
MZTForceRTR=0

; ZMV -> AVI Conversion Mode: (0 = No Video, 1 = Raw Video, 2 = Ffv1, 3 = x264,
;                              4 = XVID, 5 = Custom)
; The compression codecs can only be used if you provide them yourself.
; See zmovie.cfg for details.
MovieVideoMode=4

; Dump Audio Along w/Video (0 = No, 1 = YES)
MovieAudio=1

; Compress Audio Stream On-The-Fly (0 = No, 1 = YES)
; The compression codecs can only be used if you provide them yourself.
; See zmovie.cfg for details.
MovieAudioCompress=1

; Merge Audio and Video Streams Upon Conversion End (0 = No, 1 = YES)
MovieVideoAudio=1

;  ----
; -- Keyboard Hotkeys --
;  ----
; (you shouldn't edit these directly unless you know what you're doing)

; Super Scope Keys:
; Extra Device in Port 1/2 Cycle
KeyExtraEnab1=0
KeyExtraEnab2=0

; State Keys:
; Save State / Select Slot Menu / Load State
KeySaveState=60
KeyStateSelct=61
KeyLoadState=62
; Increase / Decrease Slot # / Direct Slot # Select
KeyIncStateSlot=0
KeyDecStateSlot=0
KeyStateSlc0=0
KeyStateSlc1=0
KeyStateSlc2=0
KeyStateSlc3=0
KeyStateSlc4=0
KeyStateSlc5=0
KeyStateSlc6=0
KeyStateSlc7=0
KeyStateSlc8=0
KeyStateSlc9=0
; Rewind
KeyRewind=0

; Speed Keys:
; Fast-Forward, Slow-Motion
KeyFastFrwrd=41
KeySlowDown=0
; Frame Rate Up/Down (Manual Frameskip)
KeyFRateUp=0
KeyFRateDown=0
; Speed Throttle Up/Down/Reset to Normal (Auto Frameskip)
KeyEmuSpeedUp=0
KeyEmuSpeedDown=0
KeyResetSpeed=0

; Pause Emulation, Frame Advance Keys
EMUPauseKey=25
INCRFrameKey=0

; Shortcuts:
; BG 0-3, Sprite Layer Display Toggles
KeyBGDisble0=2
KeyBGDisble1=3
KeyBGDisble2=4
KeyBGDisble3=5
KeySprDisble=6

; Sound Channel 0-7 Output Toggles
KeyDisableSC0=63
KeyDisableSC1=64
KeyDisableSC2=65
KeyDisableSC3=66
KeyDisableSC4=67
KeyDisableSC5=68
KeyDisableSC6=87
KeyDisableSC7=88

; Sound Volume Up/Down
KeyVolUp=0
KeyVolDown=0

; Quit ZSNES / Load Menu / Reset Game / Panic Key
KeyQuickExit=0
KeyQuickLoad=0
KeyQuickRst=0
KeyResetAll=7

; Clock Display Toggle
KeyQuickClock=0

; Netplay In-Game Chat
KeyQuickChat=20

; Screenshot Hotkey
KeyQuickSnapShot=0

; Capture SPC Hotkey
KeyQuickSaveSPC=0

; Use Player 3/4 Input as Player 1/2's Toggle
KeyUsePlayer1234=0

; FPS Display Toggle
KeyDisplayFPS=0

; Laptop Battery Display Toggle
KeyDisplayBatt=0

; Video Engine: Old/New Graphic Engine | Windowing | Offset Effects Toggles
KeyNewGfxSwt=9
KeyWinDisble=10
KeyOffsetMSw=11

; Gamma Correction Up/Down
KeyIncreaseGamma=0
KeyDecreaseGamma=0

; Movie Chapters: Insert / Go to Previous / Go to Next
KeyInsrtChap=0
KeyPrevChap=0
KeyNextChap=0

; Movie state load mode cycle
KeyRTRCycle=0

;  ----
; -- Misc --
;  ----

; Calculated Checksum & Hash: Don't Edit by Hand !
TimeChecker=223
PrevBuildNum=0

; Display First-Time Use Reminder (0 = YES, 1 = No)
FirstTimeData=1

; Prevent ZSNES from Saving the Configuration on Exit (0 = NO, 1 = Yes)
cfgdontsave=0

; - EOF -

-- 
ZSNES crashes when window is unfocused externally (by aMSN, screensaver)
https://bugs.launchpad.net/bugs/382531
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