After running stat on a mailbox in a bunch of different situations, it
looks like the problem is not that mutt is not seeing the atime
correctly, but rather it's that it's setting the atime of edited
mailboxes in weird ways.  In particular, it frequently sets the atime of
the mailbox to one second before either the ctime or the mtime
(whichever of the two it left unmodified).  Or something like that; what
it does to the timestamps in different situations seems to vary based on
factors I haven't figured out yet.

(I'm also using the final release of Karmic, and thus mutt
1.5.20-4ubuntu.)

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not seeing atime properly, keeps revisiting unmodified mailboxes
https://bugs.launchpad.net/bugs/442800
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