Going by what you pasted, your screen has three outputs; VGA-0, DVI-0 and S-video. As you can see, it thinks something is connected to S-video, and so it tries to project a cloned screen onto both that output and DVI-0 (which is also connected). As S-video can only go up to 800x600, that's what it ends up as.
Screen 0: minimum 320 x 200, current 1280 x 1024, maximum 4096 x 4096
VGA-0 disconnected (normal left inverted right x axis y axis)
DVI-0 connected 1280x1024+0+0 (normal left inverted right x axis y axis) 338mm x 270mm
1280x1024 60.0*+ 75.0
S-video connected (normal left inverted right x axis y axis)
800x600 59.9 +
Try this in a terminal after logging in and see if it disables S-video and sets your DVI-0 resolution to 1280x1024.
If it doesn't change the resolution to 1280x1024, try this instead.
$ xrandr --output S-video --off --output DVI-0 --auto
Paste your new xrandr output afterwards. If it works, we'll just have to copy and paste it into the proper file.
$ xrandr --output S-video --off --output DVI-0 --mode 1280x1024
This can *most likely* be fixed with xorg.conf voodoo; I'm just rusty in that area after not having had to touch it for a good while now. Even better, you can probably set up an udev rule (if your videocard driver permits it), but I'm clueless at that.