I was about to say that the Empeg's MP3 decoder might be more sensitive to glitches in the MP3s than WinAmp, and that the files might really have some bad frames. But then you said this:

"When I delete them and re-sync them they're fine."

And that's really scary. The files really could be corrupt. The question is (as you surmised), were they corrupted by the USB transfer process, or is the Empeg's disk bad? Another possibility is a RAM problem on the Empeg player...

Whatever it is, you seem to have gone through a good set of logical deduction steps. The glitches in the MP3s simply shouldn't be there at all if the source files are OK. I will tell you that this has never happened to me on my Mk1 player. The only time my MP3s glitched was when my hard disk went bad, and there was a span of about 2 minutes between the time that I noticed a glitch and the time when the hard disk completely failed and wouldn't boot.

___________
Tony Fabris