Have you checked the SCA gain control on the back? When we installed ours, there was a terrible gargling/whooshing noise that could be heard down in the audio region. Turns out the SCA gain was turned up so high (it shipped that way) that it was causing distortion all the way down into the audio region. Turning it down eliminated the problem.
Which preset are you using? When we first installed ours, it was very frustrating. Actually took it out of the chain and went back to our old processor. Now it's back in and doing pretty well. I'm interested in knowing which preset you're on because the limiters don't do well with some hypercompressed material. Using a preset like Cosmic may help if you have frequency balance issues. Or back off the limiters and compensate with an increase in the multiband AGC section. Also, we had to readjust all of our mic processors to eliminate voice distortino, because the Omnia handles voice much differently than our previous processor.
This is all just my perspective on the unit...there are others who may believe that a different approach is better...but Omnia support is good and they're willing to help diagnose just about any problem by e-mail.