I take it that your problem is: files that sound fine on WinAmp but sound strange played on the empeg with 2.0b3?

If that's the case, the first thing to do is to downgrade to 1.03 and see if the problem goes away. Then you know it's not the file's fault.

There is a known bug where some files might play back wrong in 2.0b3 (too loud, clipping). If, after the next beta release, the files still play back incorrectly, then make sure the empeg team gets a copy of the file to check against their new decoder engine.