First thing I'd do is log out, log back in, and check ~/.xsession-errors and the system logs (/var/log/Xorg.0.log -- really, everything under /var/log/) and see if X or the NVIDIA driver are complaining about anything.
If there's nothing in the log, you could flail around a bit. Three approaches come to mind. (You don't have to log out while you're doing any of this, but you do have log out and back in for the changes to take effect.)
First, you could move (not copy!) your xorg.conf somewhere safe (I usually just rename it xorg.conf.bak) and then run nvidia-xconfig as root to generate a fresh xorg.conf. If the new files works, you can copy anything
not related to the display that looks important from the old xorg.conf to the new one.
Second, you could delete or comment out (by adding a # to the beginning of each line) everything related to display settings in xorg.conf and see if correct resolution is auto-detected. IME auto-detection works
very well these days.
Third, you could try to force X to use the correct resolution. It's been years since I've done that but I think you could get away with editing the Device, Monitor, and Screen sections in xorg.conf like so
Section "Device"
Identifier "Device0"
Driver "nvidia"
EndSection
Section "Monitor"
Identifier "Monitor0"
EndSection
Section "Screen"
Identifier "Screen0"
Device "Device0"
Monitor "Monitor0"
DefaultDepth 24
Subsection "Display"
Depth 24
Modes "1280x960"
EndSubsection
EndSection
You might also have to edit to the Screen section to add
Option "ModeValidation" "NoEdidModes"
or
Option "UseEdid" "FALSE"
to order the NVIDIA driver to ignore the display when determining what modes are available.
Incidentally, if you aren't using multiple displays, you might want to add
Option "DynamicTwinView" "FALSE"
to the Screen section to disable TwinView. When TwinView is enabled the driver lies about the screen refresh rate, which, as I recall, breaks vsync.