I measured the gains of the various inputs and outputs and recorded the results here: http://line6.com/sup...mith0#entry4669
The Aux input should have the same gain as Guitar Normal. Guitar PAD adds about 6dB of loss at the Guitar In jack. The other differences between Guitar In and Aux is 1) the tuner is only available at Guitar In, and 2) the input impedance of Guitar In is programmable while Aux is 1M ohm. I've seen no other differences between these two.
I assume you plug the guitar into Guitar In and then Aux without changing anything else and you're noticing a difference, right? Ideas are:
1) make sure the Guitar In switch is set to Normal
2) make sure the Input Impedance is set to global 1M
If you still hear a difference then perhaps the unit is defective. I can't think of anything else to do.