so i just built myself a new test rig, with all the bells and whistles you can imagine. Syncs to anything, rotatable monitor, stereo sound with a switch to go between amplified and non-amplified (using an mcr dual amp for the amplified half). Anyway, it had a horrible interference on channels 1, 2 and 3- checked my wiring several times, swapped the board into my cab, swapped amps into my cab, changed amp chips, and everything worked fine in the cab. I finally replaced the actual signal cables with a shielded cable, and it got rid of the interference.
anyway, i'd suggest checking the shield wire and make sure it has continuity, as well as the red and black, between the ssio and the sound amp. Sound on MCR's is really picky, and i'm not sure exactly why - to me, it seems like a really odd way of doing things, but, it works if everything is exactly right......
If that all checks out, put it in test mode and go to channel test and see which channels are or are not putting out a tone- that'll make it a bit easier to tell which way to go from here.