Public bug reported:

Binary package hint: gnome-control-center

I don’t know which part of Gnome is responsible for this so I went ahead
and filed this for the settings daemon.

In Dapper I set up a whole range of Bindings with the two Win-flag keys
set to Mod4 = Super_L and Mod3 = Super_R. I mapped this via an .xmodmap
script that was somehow sucked up by g-s-d (I also mapped the media
buttons through this files).

Now in Edgy the shortcuts don’t work anymore. When I go into the gnome-
keybinding-properties and hit the Super_L + S combination what gets
registered for the command is <Mod4><Hyper>s. Upon hitting this
combination nothing happens (or, to be exact the quick-find popup shows
with the s character in it).

What’s interesting is that my Mod{3,4} bindings for Tomboy and the
Deskbar still work. Only, when I enter a new combination in Deskbar it
shows up as <Mod4><Super>a (not ...<Hyper>...). And this again
subsequently doesn’t work.

I don’t know what happened in the meantime; I cleared all xmodmap files
from the system and played with the keyboard properties to no avail.
Please advise which info is needed here. Provisionally I provide this:

*** "Alt/Win-key behaviour" is set to "Super is mapped to the Win-keys"
*** $ xmodmap -pm
xmodmap:  up to 4 keys per modifier, (keycodes in parentheses):

shift       Shift_L (0x32),  Shift_R (0x3e)
lock      
control     Control_L (0x25),  Control_R (0x6d)
mod1        Alt_L (0x40),  Alt_L (0x7d),  Meta_L (0x9c)
mod2        Num_Lock (0x4d)
mod3      
mod4        Super_L (0x73),  Super_R (0x74),  Super_L (0x7f),  Hyper_L (0x80)
mod5        Mode_switch (0x5d),  ISO_Level3_Shift (0x7c)
*** $ xprop -root | grep XKB
_XKB_RULES_NAMES(STRING) = "base", "pc105", "us,de,ru", ",nodeadkeys,phonetic", 
"compose:caps,grp_led:caps,grp:shifts_toggle,altwin:super_win"
_XKB_RULES_NAMES_BACKUP(STRING) = "base", "pc101", "us", "", ""
***$ gconftool-2 -R /desktop/gnome/peripherals/keyboard/kbd
 layouts = [us,de       nodeadkeys,ru   phonetic]
 model = pc105
 options = [Compose key compose:caps,grp_led    grp_led:caps,grp        
grp:shifts_toggle,altwin        altwin:super_win]
 overrideSettings = true


Alternative findings:
If I set the Alt/Win key behaviour to nothing ("Default") and map the modifiers 
with xmodmap like this

xmodmap -e 'clear Mod3'
xmodmap -e 'clear Mod4'
xmodmap -e 'add Mod3 = Super_R'
xmodmap -e 'add Mod4 = Super_L'

it looks like this

$ xmodmap -pm
xmodmap:  up to 4 keys per modifier, (keycodes in parentheses):

shift       Shift_L (0x32),  Shift_R (0x3e)
lock      
control     Control_L (0x25),  Control_R (0x6d)
mod1        Alt_L (0x40),  Alt_L (0x7d),  Meta_L (0x9c)
mod2        Num_Lock (0x4d)
mod3        Super_R (0x74)
mod4        Super_L (0x73),  Super_L (0x7f)
mod5        Mode_switch (0x5d),  ISO_Level3_Shift (0x7c)

Now the keybinding applet still registers <Mod?><Hyper>? even though
xmodmap doesn’t talk about Hyper anymore.

** Affects: control-center (Ubuntu)
     Importance: Untriaged
         Status: Unconfirmed

-- 
GNOME keybindings register as <Mod4><Hyper>L (and do not work)
https://launchpad.net/bugs/55729

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