If you are using the 5.1 analog outs of the dv45 into the 950's 6 channel analog in, you ARE getting some bass management in the 950. The bass from the "5" channels is ALWAYS redirected to the sub ".1" channel, no matter what position the switch on the back is in. This is the double bass thread discussed much here.

As far as the out of phase problem, I DO NOT have it, and don't understand how you guys have it.
I have a Pioneer DV-47Ai. Connected via optical, and 5.1 analog. Digital Bass Management is set to small and 80Hz. Analog Bass Management is on (rear switch). I have a DVD-Audio disc that checks the bass phase, depending on crossover point. This track is in BOTH DVD-Audio AND in Dolby Digital on the disc.
In 5.1 analog (DVD-A), speakers & sub are IN PHASE. Switching to Coax-DVD and accessing the Dolby Digital track (same as DVD-A track), speakers & sub again are IN PHASE.

Am I misunderstanding something here?