I've been working on Dethklok - Ghostqueen, and for some reason the beatmap matches the song perfectly in EOF, but is off by multiple measures in game.  Any ideas?

Usually this happens if you've added leading silence to the audio after generating the .wem file (or maybe used a different file to make the audio). Is it possible this is the case? If you're not sure, just delete the .wem from the folder and generate the .psarc with the guitar.ogg file, which should be what's being used in EoF.

Now that you mention it, I didn't add leading silence at all lol.  Got it working now!