Pj only outputs 50 or 60 frames per second, regardless of your gfx card's speed. However, if the 50 or 60 frames with AA and AF enabled is too much for the graphics card, then the play speed would slow down.
Like I explained, this is a typical example of how it works:
Start of emulation (when starting a game): set AA and AF in the settings to D3D knows to use this.
VI Interrupt (happens 50 or 60 times per second depending on if it's a PAL or NTSC rom): Send a frame to the graphics card. Graphics card enabled AA and AF on the frame. Pj wait for the graphics card to finish. Card finishes and pj continues emulation.
Now, if the card is too slow on doing its part of the processing, then pj will not be able to output 50 or 60 frames per second.