I have and issue with X windows right now where I have an extended desktop with one nvidia pci card and one nvidia agp card... both using the closed source nvidia drivers.

I installed quake 3 and when I try to play the x session blinks like it's going to go into Quake3 but then falis and all that's left on the screen is an 800x600 chunk for the desktop... you can pan around to see the rest of the desktop... but it gets stuck like that because it's trying to change the resolution to what Q3 had in it's default prefs.

This does not happen in a sinlge monitor situation on my computer... only with 2 video cards.