Do not change a thing. You have not gathered enough information. Before you make any changes, WRITE DOWN exactly what everything does. I once had a brainkiller problem in a retail speaker display room, but once we wrote down what happened when every speaker was chosen, we saw a pattern that revealed the problem: one bit in all digital addresses was stuck ON.

What IR equipment (details, please) is in between the remote controls and the IR emitters in the equipment room?

Do all three R50s fail in exactly the same way with each DirecTV receiver when controlled from the rooms? If you take a remote into the wrong room, does it affect its room exactly the same from there?

Here's one that'll kill ya: does any of this vary depending on time of day, and does daylight come into any of the rooms where the IR sensors are? Light skipping off the Pacific Ocean killed all IR in one of my systems for three hours every day, but you might have something less obvious.

Is there any source of IR in any of the rooms? An IR source in one room will affect control of all systems. (Light flashing off the Pacific is an example of that.)