I also put my spare player into my truck to test that one out running 1.02. It does the same thing.

Then this would indicate either a problem that is external to the player, or that both your players have the exact same internal fault.

Hmm. Try unplugging the tuner module and see if the problem with the aux input goes away.

Is it possible that if the player only sees the left channel attached, that it will go into "mono mode" and sent it to both and that it wont go into "stereo mode" until both channels are attached???

I do not believe this is a feature, no.

Is it possible that I am the only one that ever noticed this?

If this was happening to everyone, I'm sure there would be more complaints.

I have a very important question:

When you are playing MP3s, and you turn up your empeg's volume so that it's as loud as you can stand it, what level (what number) is displayed on the screen?

It should be very high, such as very close to 0 db. For instance, should be somewhere louder than -10 db.

If it's at a very low volume, then your problem could simply be incorrectly-set amp gains.