Xantech makes two 12 channel amps. One is plain, and the other has electronic volume controls, operated by the rc68 protocol.
The model pa1235 is the controled system. I would suggest that you take a look at what the led's on the front of the amp are showing. The installation manual gives a legend of what they should be showing.
If you find that one zone is inoperable, use your rc68 remote and an ir sensor and confirm that the zone is set to the correct ir code group, and then check for operation. Reprogram your keypad or remote depending on what you use, and you should be operational.