Not sure how much you want to pursue it.... forgive me if I insult your intelligence but im bored enough right now to just type out the thing i would try, granted i have limited knowledge of this shit compared to most....
I would burn the files to a data disc and then convert to audio CD on another computer and see if the same thing happens (good playback on computer and messed up when burnt to CD and played on other playback)
I would transfer a different show to audio CD and see if the problem is the same there. If so then it would most likely be the CD drive on your computer i would assume that is having the problem
I dont know how in the world you would fix it if any of there are the case, but at least you may figure out if its a soundcard problem, burner, or software.....
blah, blah, blah, just remember im an idiot