Wow, I had this problem once (well the bass player did) and it was well nigh unsolvable. The sound he was getting was pretty terrible (unbalanced with lots of percussive noise). He was using a Fishman, which should be state of the art. One time, someone else sat in with his bass (this was a Django reinhardt type swing band) and the problem instantly went away.

We eventually figured out that, although our bass guy was well-skilled he simply played TOO HARD for the pick up to be effective. This probably won't help your situation, but our bass player had to revise his style a bit and play softer. The problem went away.

Keeping in mind that his HARD style came from years of Bluegrass playing where he never had a pickup and rarely even had the bass miked.

I play guitar pretty hard as well, and sometimes have "overdriven" Piezo pickups.

Rick