I haven't ever encountered that. If your CD player was stopping and re-starting the digital signal or your digital audio cable was somehow defective, the 950 would lose and re-acquire the signal between tracks. That loss of signal would typically appear as a brief muting, not a thump.
There is a "format lock" option that will allow you to disable the 950's digital signal auto-detect for that input. It would essentially force you to specify one decoding mode (such as "Pro Logic II" or "stereo" for CD listening) for that input, but it eliminates the audio "pause" and would likely eliminate this thump. It's described on page 31 under the heading "Surround Data Format Lock."
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