Sean, the problem apparently manifests itself through the SD outputs then creeps up through the HD outputs is my best guess since my recording was hosed and the HD was ok. I have my stb set to always output 1080i and the 4:3 is set to Pillarbox/Letterbox.
I can't test this for sure, but I have had instances where the HD was stuttering and it started right away, I don't know what causes it, other than extremely heavy use of the EPG. I know the Dish 501 used to throw fits if the EPG was heavily used, it seems the stb programmer's cannot cleanup the GUI memory very well when switching between Video and GUI.