Trouble shooting Update:
I obtained a IR reader to see if maybe it was sending the wrong code during the times it was not responding -- No IR output when this is happening.
I also noted that when it is happening, a headset plugged in to the remote has the same problem - no volume control or mute function. so this pretty much points to an internal problem with vol, Mute, and TV power, as thest functions for the headset have nothing to do with the TV brand/IR code set in use and will only apply to the ROKU hardware.
I haven't done programming professionally in awhile but I bet this could be solved pretty quickly. Somehow, just those functions are being treated differently than the normal ROKU functions and getting hosed.