you might use the ViewPort item in your xorg.conf:
Modes "1280x1024" "1024x768"
Virtual 400 200
or something similar. the 400 is the x-offset and the 200 is the y-offset. this specifies the upper-left corner of where xorg should paint your screen, relative to the absolute upper-left of the monitor, which may be off the physical screen, as your setup is using. Play with the numbers, I don't know how far off yours is. remember you can kill X with Ctrl+Alt+Backspace and return to the command prompt to fix things up. this adjustment would not affect your text-mode command line display since X is not the one rendering that.
never tried it myself but it might help you!