"But it was so easy! I brushed the whole cluster into
the box in 3 swipes, leaving only the airborne ones.
Is it possible the queen took flight as I was dumping
them in? And why, then, did the bees wait a few
minutes to come out of the nuc box, after acting so
much like the queen was inside?"

There could have been many reasons. Maybe some smell they didn't like, or
the scout bees insistant, or whatever. Unless I'm different that the
others who have been hiving swarms for a couple decades, you're going to
loose a percentage. I've had them take off after several days seemingly
happy in the hive.

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