Thanks for all your help!

I still have remaining questions for the empeg guys if they ever see this:
- Is it true that the issue is that the Empeg's DAC is a CD-player DAC which can only accept 44.1khz properly, and that the player software has to do a sample-rate conversion to get it to play on that DAC?
- Does anyone know of any other hardware-based MP3 players that will have the same problem?
- Can anyone think of other situations where a 48khz MP3 file will play back poorly on other kinds of equipment?

By the way, the mixing session that brought all of this up in the first place, was for this video:
https://www.youtube.com/watch?v=_f1doSfY2pQ