I've got it too. I have an ICBM btwn my 950 and Earthquake Cinenova Grande and Audiosource Amp3 (for back surround) amplifiers. I get the thump from by back surround speakers, nothing from the speakers connected to the Earthquakes.
950 is set-up as all Large, Sub on (all x/o set to 120, which shouldn't matter, but someone said the 950 high-pass filters the LFE at whatever the x/os are set to. I assume this isn't the case if speakers are set to Large, but whatever). ICBM x/o is rear and back surrounds: 80hz, center: 60hz, front: bypass for 2-channel or 40hz for HT.

FWIW, the thump really only became objectionable when I connected the ICBM, which forced me to combine both L&R back surrounds into one channel in the ICBM and then resplit the signal at the amp. Makes sense that the resulting thump would be roughly twice as loud. Before I barely noticed.

And, for the record, the thump happens every time the 950 engages the digital-muting. So, if there's a ~3 second silence in between tracks on a CD (and I'm listening via digital instead of analog connection), I'll get the pop. Becomes really annoying during listening sessions, so much so that I've added an external DAC to my list of upgrades. Hopefully after christmas, I'll no longer be using the 950 digital input while CD listening.