I believe that i just found a temporary workaround.

Since the flickering seems to be caused by the automatic mode detection
on my non-connected VGA output, I used xrandr to force a mode on that
output.

I used the following commands

xrandr --newmode dummy 75.00  1280 1301 1333 1408  800 804 808 816 -hsync -vsync
xrandr --addmode VGA dummy
xrandr --output VGA --mode dummy

Those commands cause a lot of flickering but after them, flickering is gone.
  
The result can be verified with 

 $ xrandr --prop | cat -n
     1  Screen 0: minimum 320 x 200, current 1280 x 800, maximum 1280 x 1280
     2  VGA disconnected 1280x800+0+0 (normal left inverted right x axis y 
axis) 0mm x 0mm
     3     dummy          65.3* 
     4  LVDS connected 1280x800+0+0 (normal left inverted right x axis y axis) 
261mm x 163mm
     5          EDID_DATA:
     6                  00ffffffffffff0006af142100000000
     7                  010f0103801a10780a30259855548827
     8                  24505400000001010101010101010101
     9                  0101010101014c1d0080502010301520
    10                  440005a3100000190000000000000000
    11                  00000000000000000001000000fe0057
    12                  35333832004231323145570a000000fe
    13                  00fffdf3e9bb8d6f0001010a2020005f
    14          PANEL_FITTING: full
    15                  supported: center       full_aspect  full        
    16          BACKLIGHT_CONTROL: native
    17                  supported: native       legacy       combination  
kernel      
    18          BACKLIGHT: 0 (0x00000000) range:  (0,0)
    19     1280x800       65.3*+
    20     1024x768       60.0  
    21     800x600        60.3  
    22     640x480        59.9  
    23  TV disconnected (normal left inverted right x axis y axis)
    24          BOTTOM: 37 (0x00000025) range:  (0,100)
    25          RIGHT: 46 (0x0000002e) range:  (0,100)
    26          TOP: 36 (0x00000024) range:  (0,100)
    27          LEFT: 54 (0x00000036) range:  (0,100)
    28          TV_FORMAT: NTSC-M
    29                  supported: NTSC-M       NTSC-443     NTSC-J       PAL-M 
      
    30                             PAL-N        PAL         


The interesting line is 3 which indicates that my "dummy" mode is activated for 
the VGA output.

PS: I used a 1280x800 mode because this is the resolution of my laptop
panel and, somehow, using a smaller resolution caused my gnome panels to
be resized.

-- 
Flickering with version 2.4.0
https://bugs.launchpad.net/bugs/256142
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