Shane, how are you wiring these?
I used to own some and could somewhat create the situation you describe. Inside the pack, there are 6 power connections, one for each channel. The channel dimming control circuitry is arranged in pairs, however. So the dimming control on channel 1 works for channels 1 and 2. It turns out, those pairs of channels have to be on the same phase to work properly.
I originally tried to wire mine for single phase operation with channels 1-3 on one leg and channels 4-6 on another. All I got was a flickering, misbehaving mess on the middle channels. After I divided the channels into groups of channels 1-2 and 3-6 things worked properly. I just ended up wiring each pack opposite--switching legs back and forth so the load stayed even.
If you're wiring them normal 3-phase, with channels 1-2, 3-4, and 5-6 grouped as such, then you should be fine, and I have no idea what's wrong.
Edit: maybe something in the control circuitry overheated?