hi there ...

I´m in nearly the same situation, my Apple Cinema Display only works on it´s native resolution and I cannot use most of the programs fullscreen ...

But for Smoking Guns can also run in a window, just open the DEFAULT.CFG and find this part :

seta r_mode "4"
seta r_fullscreen "1"
seta r_customwidth "1600"
seta r_customheight "1080"

to :

seta r_mode "-1"
seta r_fullscreen "0"
seta r_customwidth "640" (or whatever you want the window size to be)
seta r_customheight "480" (see above)