I agree with Carl -- time is out when the umpire is doing something other than watching the game. That applies when s/he's cleaning the plate, catchig foul balls that are being thrown back in, returning from the infield to the plate when doing single-person umpiring, ...
One thing that I do to make this clearer is to overtly call "time" the first couple of times the situation arises during the game. It's not too loud -- just loud enough for the closest players to hear. And, it's accompanied not by the two-handed "touchdown" signal, but by a one-handed "stop sign" signal.
After the first couple of times, I just revert to a more non-chalant version of the signal. When asked, I can claim that I've been calling time on these situations since the beginning of the game.
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