I had a somewhat different problem. No audio from my guitar. I have an original iPad (1) and just got a new iPad-3 Retina. I purchased the iRig STOMP and downloaded the Free Amplitude app. I hooked everything up per the manual. No problem first time through using the iPad-1. Then put it away for a day (this fact is important).
A day later, I bought the iPad IK Amplitude app (@50% off!). After registering my new purchase, I hooked eveything back up (using headphones). But...no audio out from my guitar. Not even the metronome or demo sounds. Although the red light on the STOMP box was lit, and all settings were good, nothing. After trying various things (e.g, Mono was set to off, connections secure, checking cables for headphones, guitar), and still no audio, I thought, "...what about the STOMP's 9V battery?". I had just put this battery in the previous day, and it worked fine.
So it couldn't be the battery, right?
Wrong. I must have left the system connected that first day. I removed the 9V batter from the STOMP, and gave it the old "tounge test"; i.e., place the 2 terminal ends of the 9V battery on the tip of your tounge and see how much "tickle-shock" you get. Well, I didn't get much tickle-shock (new 9V batteries should give quite a shock to your tounge). I had a brand new 9V Durcell battery still in the package, so I tounge-tested it and got quite the tickle-shock!
Using more conventional methods, I used a voltmeter to test both the original STOMP battery and the new 9V Duracell.
My tounge didn't lie. The meter showed the original STOMP 9V battery was close to dead; only reading about 4.5V (should have been close to 9V). The new Duracel 9V pegged the meter at 9V! And the STOMP original 9V battery had very little amperes (my voltmeter needle barely moved with the original STOMP battery, where as the new 9V showed a healthy 500 milli-amp hrs (mAh).
So...there was really no clear indication given from either the iRig STOMP box itself (red light seemed to shine as brightly as the day before)...nor any indication from the iPad that the battery on the STOMP was close to dead.
How I fixed my problem: I replaced the dead 9V battery on the iRig STOMP with a fresh one. Once I did that, everything worked fine.
Note to LK tech: I have Line6 wireless equipment to xmit my guitar feed wirelessly to my amp. They have a nice feature that lets one visually see on either end of the wireless system when the batteries on the wireless pack that's connected to my guitar are failing (but are still working). They change the color from green to orange to red. This would be a nice feature to have on the iRig STOMP (next time I'll use a 9V AC adapter connected to the iRig STOMP box).