So, I have a nvidia Twinview setup (since nvidia do not support proper xinerama) which gives me to some issues.
By default, if I do nothing (just wipe config.ini) I get fullscreen spanning two different-sized monitors, with the login button off the side and inaccessible due to being outside a smaller monitor.

Window mode works quite fine.

If I use the
xsize=1920
ysize=1200
xf86vidmode=0

settings, I get interesting results. The vidmode is fine, but the window isn't registered, so keypresses end up in the terminal below the window, and neither alt-tab nor anything else can sort this out for me (window isn't displayed as existing in alt-tab ) and I cannot change out of it, since alt-return gets fed to the terminal that has keyboard focus.

So, I guess I could just ignore my lovely dualscreen setup and write it off as a luxury problem, but well.

some system specs:
Fedora 14, Gnome, Metacity with Composition enabled.
x86_64
NVIDIA UNIX x86_64 Kernel Module 260.19.29

I use the same config.ini tweak with the numbers for my preferred screen and then start it in windowed mode. I then move it over to the screen I want it on, and then use my window manager (IceWM) to fullscreen it (Alt-F11 in IceWM). The result is I get a fullscreen VO in just one of the monitors with everything the right size.

I don't know if Gnome lets you fullscreen arbitrary windows like IceWM does, but if so, it would be worth a shot since you said windowed mode works fine.