I'm having the exact same problem, and better yet, it's intermittent with absolutely no apparent cause; sometimes it works fine, but far more often the right audio doesn't record or sound at all. I have excellent equipment for recording, and have tested rigorously to ensure that it has nothing to do with computer speakers. I have emailed the support adress, and it's been a week without response (Which is understandable, I suppose). I have rigorously checked every possible option in the program, and there is NOTHING that has anything to do with input or speaker balance while recording that I have seen.
I bought this program and have since been trying to use it for months, and it is a wonderful program, minus this severe and glaring issue that is seriously impeding my recording. Please inform us of a manner to solve this problem.