There is a known bug in 2.0 emplode, where tags with extra-long comment fields will mess up the synch, although I think your problem is different because it's happening on the player itself.

You could be correct in stating that the album-art data is making the files look invalid to the decoder. Stick enough junk in a file and the decoder might choke on it.

First, use MP3Trim to examine the file and see if it gives it a clean bill of health. If not, clean it up (re-save it in MP3Trim) and send it to the player again. (edit: Note, make sure to replace the tune by right-clicking and selecting replace tune, otherwise you'll have two copies of the file on the player.)

NOTE: Make sure to keep a copy of the "bad" version of the file. If it's a valid file but the new decoder chokes on it, the empeg guys will want a look at it.