STO does indeed have a little publicised 3D mode that works in conjunction with features on compatible NVidia cards. It could be a driver settings issue, as the 3D mode setting has been reported as changing during o/s patching.
You may not see it enabled outside of STO for the reason that your other applications may not have been written to access these features (i.e. its not a global - apply to anything on the display).
This thread may help. http://sto-forum.perfectworld.com/sh...php?p=13086351