Hmmm - well you would need to read up Section 6 of the manual (Edit: its for the config - inputs/outs). Even if you had an dual tone panned patch with only one of the tones selected, head phones should have picked up the stereo.
I'm am not going to suggest you open 'er up. Sometimes if the tuner doesn't see a signal it can point to a bad jack. But you have signal in.
But check your cables, batteries (if active PUs) and then connect the unit to Gearbox and see what the patch settings are.
If nothing checks out you will have to reflash the unit and hope that does the trick.
After that its submit a support ticket to the L6 Mothership time.