I have this problem too with my 1 Ghz 17" iMac. I'm using external speakers and every now and then, I notice the sound suddenly come mostly from the left side. I open the system preference and, like you, the balance has changed itself toward the left.
I checked the prefs for corruption but found nothing wrong. The problem persisted with every OS update, up to 10.2.8, which i'm currently using. I'd have to try with a new user account to see if the problem continues, but seeing that I'm not alone with this problem offers some hope...