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.