I had the same problem with my OB-Xa (one tray was louder than the other). It took two techs to figure it out, but the final solution seemed to require using different resistors on the individual tray outputs until the levels roughly matched. It wasn't a real "fix" in that they never figured out what caused it, but it worked. The fact that yours is doing something similar seems to be symptomatic of a specific issue. 

The other, much simpler method would be to pan the upper/lower tray to the left/right outputs, respectively, and then match the levels on your mixer. I think this is what the other poster might have been suggesting. Simple, but effective.