I've seen this happen quite a few times with my Remote, where I'd press a button to activate some train function, or thumb wheel a speed change, and the Remote seems to go to sleep, or looks like it wont respond.
I believe it has to do with poor signal issues, where a Command goes out, then the TIU/Remote sits waiting for a Response, but one never comes. So its sits in limbo until it times out on the Command, then allows further action.
I had one engine where sluggish Remote action was very apparent (and quite annoying). So I took this engine and did a wholesale clean up job on wheels, pickup rollers, and tender axle pickups. I attacked wheels and pickup with a Dremel soft wire brush, alcohol, and a ton of Q-tips.
Guess what, the sluggish Remote action disappeared from this engine.
My gut tells me unless the Remote/TIU is failing solid, across all engines, and areas of track, it's NOT a hardware problem, but there are signal issues in play here...