For ther record, The Dish Network UHF remote controls are SIMULTANEOUS IR/UHF (i.e. they send out both IR and UHF codes when you press a button). So, that is not the problem.
To further reinforce the fact that that is not the problem, I operate the system with a Pronto TSU2000 and have tried to operate through the IR receiver in the keypads with the Pronto remote (which it does in the room and with my Xantech IR system), it repeats all the functions on the Pronto I've tried except the Dish codes (doesn't even blink the IR confirm light on the keypad (once again, it does on the old style Russound Keypads I have on the same system AND on my Xantech system upstairs)).

Dave