Running Hardy Alpha 5 with latest updates.
I am still seeing this bug or so I think...
Here is my setup : A laptop in its dock with an external monitor plugged on the DVI port of the dock. The "native" resolution of my monitor is 1280x1024@60hz
But in fact, I only get 1152x864@75Hz (I can change it using the Gnome RANDR applet for example).
Here is the output of xresprobe :
$ sudo xresprobe intel 
id: 
res: 1280x800
freq: 
disptype: lcd/lvds

xresprobe doesn't seem to see the DVI monitor.

Here is the output of ddcprobe (seems fine) :
$ sudo ddcprobe
vbe: VESA 3.0 detected.
oem: Intel(r)GM965/PM965/GL960 Graphics Chip Accelerated VGA BIOS
vendor: Intel Corporation
product: Intel(r)GM965/PM965/GL960 Graphics Controller Hardware Version 0.0
memory: 7616kb
mode: 1280x1024x256
mode: 1280x1024x64k
mode: 1280x1024x16m
mode: 1024x768x256
mode: 1024x768x64k
mode: 1024x768x16m
mode: 640x480x16m
mode: 800x600x64k
mode: 800x600x16m
mode: 640x480x256
mode: 800x600x256
mode: 640x480x64k
edid: 
edid: 1 3
id: 3514
eisa: AUO3514
serial: 00000000
manufacture: 1 2007
input: analog signal.
screensize: 26 16
gamma: 2.200000
dpms: RGB, no active off, no suspend, no standby
dtiming: 1280x800@59
monitorid: AUO
monitorid: B121EW03 V5

Here is my xorg.conf :
$ cat /etc/X11/xorg.conf
# xorg.conf (X.Org X Window System server configuration file)
#
# This file was generated by dexconf, the Debian X Configuration tool, using
# values from the debconf database.
#
# Edit this file with caution, and see the xorg.conf manual page.
# (Type "man xorg.conf" at the shell prompt.)
#
# This file is automatically updated on xserver-xorg package upgrades *only*
# if it has not been modified since the last upgrade of the xserver-xorg
# package.
#
# If you have edited this file but would like it to be automatically updated
# again, run the following command:
#   sudo dpkg-reconfigure -phigh xserver-xorg

Section "InputDevice"
	Identifier	"Generic Keyboard"
	Driver		"kbd"
	Option		"XkbRules"	"xorg"
	Option		"XkbModel"	"pc105"
	Option		"XkbLayout"	"fr"
	Option		"XkbVariant"	"oss"
EndSection

Section "InputDevice"
	Identifier	"Configured Mouse"
	Driver		"mouse"
EndSection

Section "Device"
	Identifier	"Configured Video Device"
EndSection

Section "Monitor"
	Identifier	"Configured Monitor"
EndSection

Section "Screen"
	Identifier	"Default Screen"
	Monitor		"Configured Monitor"
	Device		"Configured Video Device"
EndSection

Here is the ouput of xrandr -q :
$ xrandr -q
Screen 0: minimum 320 x 200, current 1280 x 864, maximum 1280 x 1280
VGA disconnected (normal left inverted right x axis y axis)
LVDS connected 1280x800+0+0 (normal left inverted right x axis y axis) 261mm x 163mm
   1280x800       60.0*+   60.0  
   1280x768       60.0  
   1024x768       60.0  
   800x600        60.3  
   640x480        59.9  
TMDS-1 connected 1152x864+0+0 (normal left inverted right x axis y axis) 376mm x 301mm
   1280x1024      60.0 +   75.0     59.9  
   1152x864       74.8* 
   1024x768       75.1     71.9     70.1     60.0  
   832x624        74.6  
   800x600        72.2     75.0     60.3     56.2  
   640x480        75.0     72.8     66.7     60.0  
   720x400        70.1  
TV connected (normal left inverted right x axis y axis)
   1024x768       30.0  
   800x600        30.0  
   848x480        30.0  
   640x480        30.0  

I have also attached my Xorg.0.log

PS : If the external monitor is plugged on the VGA port, it works like expected.