Make sure your cable box is set for optimum stereo in it's menu or turned all the way up and never use the volume control on the cable box remote.
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I experience the same problem with my 2.1 video set up.
I run DirecTV digital out to a MD10 virtual surround DAC/PRO decoder.
One channel will disappear and come back if I raise the volume a little.
I use the analog pass through on a Parasound AVC 1800 for the Left - Right - Sub output of the MD10.
My next step is to lower the level controls on the Parasound amps in order to raise the volume level higher on the pre/pro and see if this solves the issue.