There will be some imbalance if you have a lot of gain in the signal chain, which is why I suggested just the iPhone into the SEX amp.
If just the iPhone into the SEX amp still results in channel imbalance, you can swap the tubes to see if the imbalance follows a tube (I suspect it will not).
Beyond that, we can see where the imbalance is entering the amp by playing a 60Hz tone into the amp with the volume pot half way up and measuring AC voltages at a few places. When you're all setup for that, let me know and I can write down some steps.
-PB