Thanks guys. It sure sounds better switched in towards the knob, as it's unbearably "thick" the other way and the HPF doesn't seem to do as much. Still, enquiring minds...
When I get the answer, I'll put a dab of paint or nail polish by the "in phase" position just for troubleshooting purposes. I remember once on the Headway it had been sounding brilliant for weeks, then one day I showed up to the gig in a familiar room and it sounded absolutely like crap and I couldn't figure out why. Turned out it was phase reversed, but it took a while to find it.
Chris-- the only reason for things sounding different as a result of flipping the switch would have to do with interactions between the amplified sound and the bass. For example, if you played the bass in one room and had the rig in another, changing the polarity should have no effect at all. That is, unless there is something wrong with the circuit or it's poorly designed. I know that there are op-amp designs where I could see that happening but, as we all know, none of that applies to the fdeck gem.