I'm having a similar issue on a fedora box, only over VNC. has anyone else seen this?
when i type my keypad keys (and enable input logging) it shows they come is as shift+(their non-num lock function) so for example 2 is (shift+down).
This is with numlock on, with numlock off they take on their non-numlock functionality (2 is just down).
I commented out the shift+(x) functionality in the key definition file and now i get the straight numbers in, but i can't do shift down, up, left, right, pgup/pgdn etc etc.
This is on a VM, and on the console it does not behave this way just over VNC.
also other text editors don't have this problem over VNC.