Keta,

The first thing I'm curious about, is how you have your system configured to send only the LFE to the sub amp when in 6 CH BYPASS?

The second issue regarding phase alignment between your mains and sub is that, unless the mains and the sub are exactly the same distance to your meter, you're not likely to ever have the phase correct if you only have a normal/reverse phase switch as your tweak.

There is definitely something at play when switching from the digital filters of the 950 to the analog filters. Exactly what the answer is was never arrived at, at least to my satisfaction.

I personally think that the problem arises from the way digital BM works, creation of a duplicate signal for each channel, 1 that's HP filtered and the duplicate that's LP filtered (selectable triple crossover), volume adjusted and sent to the summing block to be combined with the LFE signal, which has a global, 120 Hz LP filter applied.

Analog BM is a simpler 80 Hz HP/80 Hz LP Linkwitz/Riley active crossover.

Other issues include whether or not your player applies a global LP filter to the LFE signal in the digital output vs. no filter on the analog LFE output.

The fact that some people experience the phase shift when switching from digital BM to analog BM and some do not, indicates that placement distance differences and/or player/950 cascading filters probably have the most to do with the answer, because there's no way I believe that some 950s have properly wired analog crossovers and some do not.

As far as the setup discs that are currently available for multichannel audio systems, I'm not a fan of any of them.

I just use a SACD MC disc that has good LFE content and repeat a track that has a bass line intro and play, meter, reset and pause, adjust phase and repeat until the reading is highest, with the SPL meter in my listening position.

BTW, I don't see a difference when switching back and forth because I keep my 950 in 6 CH BYPASS mode all the time.