Chester,
I agree, this entire site is an awesome source for gadget-geek info. As far as our mods go, I'm almost certain I noticed this before I added IR mods. Also, in Jay M's response to this post he indicates he has a relatively new DishPlayer.

Food for thought: Could it be specific to one or two channels? Next time I catch it I'll make note of the channel number.

Of course it might be easier to call DishNetwork--not that I've EVER gotten an answer out of them that didn't sound like complete and total BS.