Running in a window will get you up and playing again. Edit this config file: UrbanTerror\q3ut4\q3config.cfg
seta r_fullscreen "0"
seta r_customwidth "800"
seta r_customheight "600"
These settings switch off full-screen mode and run in an 800x600 window. You will probably want to increase the window size if you have space. Once you are running you can try pressing control-enter to switch back into full screen mode.
I also run dual-monitors and UT automatically runs full-screen on my primary display. There must be some subtle difference between our monitor configurations. I have a taskbar only on my primary display and extend my desktop onto the second one. If you're running dual-monitor software that spreads the taskbar across both screens (making Windows think your two displays are really one) then switching that kind of stuff off might help.