Sounds like the assign buttons are messed up on the patch you are using. On the channels that are problems are they assigned to main output left/right ? Is the little light that indicates this illuminated on the channels?
Did you try to use the factory default setting and testing the outputs from that setting? The factory default is the setting on shows, all the way on the left.
There is a factory RESET button, but I would recommend you do this only if instructed by tech support. This will require a reload of the firmware.
Power off
Insert iPad
Find small recessed button between power and the ethernetconnector.
Depress that switch using a pen or toothpick or some small pointy object
Power on while holding down thr swith for a few seconds or until the update firmware prompt shows up
Then follow the prompt to update the firmware.
I would only do this while on the phone with tech support, as they can guide you thru the process and possible help resolve the issue without going thru the whole ordeal, plus that puts you on record with this problem .