are you sure it is the pickup? What you describe sounds like issues that some folks have with the saddle piece not contacting the bridge with even pressure. Graphtec makes some saddles that have standoffs at each string on the underside so that you can 'balance' the kind of problem you describe. Here's the saddles I'm referring to:

http://www.graphtech.com/product-209-2/

What you can do with that saddle is sand the underside flat by flat, to get a balanced output from the transducer. This was designed for undersaddle transducers, but might work for LR Baggs type as well. The fact that you can move the baggs around easily is a bit of a concern actually. It could simply be that you aren't getting even transduction into the Baggs due to the way it's attached to the underside of the bridge. Maybe more 'stickem' is needed on the ends.