There are 2 types of FPS that people here seem to get mixed up.
1. The game is running full speed in the background but you only see half the frames (the 'normal' type).
2. The game is running slowly and each frame is the real speed of the game.
Obviously the frame rate of the first can be set to what ever you want (which I'm assuming what the OP thought PCSX2 was using). You can't do anything to speed up the second without speeding up the speed of the actual emulator.
I also might be completely wrong, but the theory seems good enough