Not sure what changing to Speed mode is going to do for the issue. Since it most certainly should work in normal mode, and certain commands require feedback from the locomotive anyway, you're not solving any problems, maybe just partially masking them.
At this point, I have no idea what is going on with the TIU. The fact that tethering it doesn't change it seems to eliminate RF issues between the remote and the TIU. My next attempt would be to try a different remote, but since it works with the Rev. L TIU, that's probably not the problem.
I'm at a loss at this point what could be doing what you see.
In speed mode the remote doesn’t wait for answers from the TIU or engine, can’t remember which. Either way I though if it worked in speed mode that might tell us if the transmit part of the TIU is the problem. I guess it only matters if there is an ACK/NAK process that happens when the remote is in normal mode.
Another thought, I don’t know if the TIU transceiver boards are universal across revisions of the TIU but if they are OP could try to swap them between TIUs and see if the problem “moves” with it.