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.
Ah, I figured it out. For some reason running a cpu miner at the same time caused the speed to drop, but only when the console window running the GPU miner was in the background.
Since the gui didn't have the console window it got treated as always being in the background and wouldn't run at full capacity.
I didn't notice it before because I always had the GPU miner in the foreground.