Which headphones do you have? If you have HD580/600/650, I would recommend unplugging your headphone cable from your headphones, plugging the cable into the amp, then measuring the AC voltage at the headphone end of your cables.
The good news is that your Crack has no channel imbalance to speak of. The bad news is that it's either your headphones, source, headphone cables, or you still have an installation issue with the padding resistors that go on the pot. (maybe post a pic?)
-PB