All I can think of is, in a 21st century system using an HDMI matrix, why are you messing around with 1980s IR extender type systems? In what likely is a fairly high budget set up, you are using low-budget componentry. Sorry to not offer any answers to your questions, I would be inclined to step back and take a second look at the design here. Are RF or IP remotes not possible?
There is no truth anymore. Only assertions. The internet world has no interest in truth, only vindication for preconceived assumptions.