I've heard the Berning break in on a Acoustat 1+1 - a difficult load - and compared with the Pass Aleph 3 at the same time. On bass its not the Berning, and very doubtful that its a reliability issue.
Although I agree that cabling is not something to jump into until a few other things are tried, my strong gut feeling is that you are finally hearing that Type 4/PBJ. That coupled with the breakin - the Berning I listened to was thin but clear, no glare at the beginning - could very well cause your problem. Spatial and harmonics can be greatly improved by NOS inputs - and you've gotten some fantastic advice here and I wouldn't hesitate eventually going that way - its still, at this point, not going to solve the bass issue you describe.
Since you can always sell the Berning at not too much of a loss, investing in bringing up the rest of your system should not be ignored. Biwire is tough at $500. Ask around. You can send unit back to Berning if that would make you feel better, but I think you are just going to hear that its ok and then be really discouraged.
The Berning is a very high end amp and when you move into this kind of piece, the rest gets exposed. Please keep us posted.