The IR system is totally separate of the video/audio parts of the system. I never once used the IR functions and all worked well… as long as it worked.
We found the biggest culprit was the individual receivers at each TV. Over the years I used the system I replaced all three receivers (network balun devices), one of them more than once. I bought them from Pace Electronics for $50 each.
The Matrix power supply is a leading cause of issues as you’ve found out. But in my case that never caused my problems. I bought one from Pace and when it didn’t help they took it back. They even sent me a new Matrix box to test out but when that didn’t help they let me return that, as well.
Another common weak link is the HDMI cable from the receiver to the TV. So don’t be afraid to try a new HDMI cable.
After 4 or so years of struggle I kept the system in place but stopped using it. We were streaming all of our TV so I put a Roku device on each TV and stopped messing with the clunky Matrix system.
PS. Never buy these parts from Winnebago, they will overcharge you terribly. For instance the new Matrix box was over $700 from Winnebago but only $250 from Pace.