Yeah, I love both the JB and the Distortion when they're paired in the right guitars. I've had similar results like you have where the Distortion worked great in one guitar and just didn't click for me in the next one. It seems like it does walk a fine line where brightness is concerned, if the guitar tends to be a bit on the bright side naturally then the Distortion can be a bit much, at least for my taste.
The pickup that I found a while back that really satisified my desire to have a JB style of tone but without some of the negative attributes was the Duncan Alternative 8 pickup. It's got an alnico 8 magnet in it, has plenty of output without feeling overbearing. Nice top end that feels a bit smoother and sweeter, and doesn't have the harsh upper-mid spike that the JB can have. In a lot of ways the Alternative 8 feels to me like my "alternate universe" version of a JB, if that makes sense? So for future reference that might be a good one to check out too.