Just finished a customers house with the CA 6.4 LCD system and Dish Network satellite receivers. Customer also has 4 one-for-all universals and a ProntoPro. He ha two Dish receivers in his main cabinet, including a 301 and a 501 on different addresses. ALL remotes work fine in all zones. We even have double emitters, as we're actually controlling more devices than we need to (long story)...
Have noticed some general issues with DISH IR though IE: Some Pronto and other remote programming works great in one system, then not worth a #$#% in the next...I have found that a LOT of patience and teaching the codes VERY carefully and testing them ALOT have been the only ways around it.
I do know that several of the IR commands are issued on the RELEASE of the remote button, not the press. Experienced this EXTENSIVELY with the Inteelinet RS-1000 system....had to program about half them buttons to issues the ir on the release and not the press...
AVDUDE "It might work better if it were plugged in and programmed first...just a thought!"