That's odd... you're using the same flags in both cases? If so, can you try running the poclbm.exe that comes with the GUI and see if that does the same thing? I don't have an Nvidia card to test on but I haven't heard of anyone else with your problem.
I have a problem with the gui, it only seems to max out the GPU at around 30% even though the non-gui version maxes out at 100%
I'm using an Nvidia card with the latest drivers and windows 7.