Hmm, reading through some of the posts in this thread has me wondering whether it was just being overdriven on the input side, and we needed to engage the 15db pad to keep the amp from going into protect mode due to a clipped input stage?
http://www.talkbass.com/forum/f15/ampeg-pf350-500-part-vi-942247/index4.html
Honestly, I've never had to do that before with my L2000 with its stock onboard preamp... And it didn't sound clipped at all while it was working. I guess if we end up using that amp again (with a back-up next time of course) it's worth a try.
The rev a, through rev c models were known to have this problem. Do you know what rev it was?