Are you also occasionally getting hard disk errors? Someone else has reported that a dry solder joint on his IDE header was responsible for both the hard disk errors as well as some noise issues.

Anyway, your diagnosis that it's a loose solder joint sounds likely, so yeah, look for that sort of thing. Post pictures if you find it, because you're not the only one reporting problems with one of the two audio channels.

Note that it could be very very small and hard to see. If you've seen the pictures of the IDE header problems in the FAQ, you'll see what I mean by small.