I have no idea what causes this, but I had this happen to me once, and it was also when I was running with separate front / back EQ settings. It only happened once though, so I never posted anything about it. I just chalked it up to a stray gamma ray or something.

It was exactly the same as what you describe. I booted it up, and it sounded completely and utterly wierd. And as soon as I made the first adjustment on the eq, Bam! It just snapped right back to normality. Very odd.

Mine was a while ago, I think it was with 2.0b3...? Can't remember...