Ben

If you have flashed the firmware you could try a global settings reset.    Hold down the 'left' button on the directional keypad and power up the Pod.   This does a global settings reset and can occasionally help.  It is also useful if the preset you were working with was corrupt as it jumps you back to patch 1A.  If you use this, you will need to check your global settings to make sure they are how you want them.  You will also need to recalibrate your expression pedal (details here --> http://line6.com/support/docs/DOC-2223).  None of your homemade presets will be lost but your setlist names will be renamed to the default names.

Frankly though, it sounds more like a cable/connection issue to me.   Suggest:

1)  Try different XLR cables/inputs on the mixer.

2)  Try it with the 1/4" Outputs ... any better?  Again, consider cables and connectors.