The Japanese version (PAL) runs at 24 frames per second and the US version (NTSC) runs at 29.97 frames per second. In order to get them running at the same speed, they spread 4 PAL frames out over 5 NTSC frames (
telecine). This is close, but they still end up with about a 4% speed difference, which is what you're seeing (should be out by 1 minute after 25 minutes). It's too small to notice unless you're running them side by side.
If you want to watch for inconsistencies, you'll have to play them at the same speed. There's probably a player that will do this. Windows Media Player 10 has a
speed adjuster, but I'm not sure how fine the settings can be. VLC has lots of options, but I can't see a speed finetune after a quick look through the settings.