I have the same problem on the same machine. I also have the same problem while playing Sherlock Holmes and Clash of the Titans, although in this case, it isn't as drastic as with Prince of Persia Blu Ray.
having problems with the Prince of Persia Blu Ray disc? I have a BDP-1600 with the latest firmware (v 2.12). When I play the disc, it works fine for five minutes or so and then the video freezes for a few seconds. Once it unfreezes the audio is out of sync. with the video. It's as if the audio keeps running (though I can't hear it) while the video is frozen. After 30 seconds or so, it resynchronizes and everything's fine until it happens again in another two to five minutes. While the audio is out of synch., the video jitters a little, too. As if it's catching up? Very strange. I've tried two discs from Netflix so it must be some kind of compatibility problem.
using bdp-2500 ,windows xp 2nd edit