not seeing atime properly, keeps revisiting unmodified mailboxes

Eek -- that first line should have read "In karmic beta". Sorry for the confusion! Jaunty's mutt works, Karmic's doesn't. Launchpad doesn't seem to have a way to let me specify which Ubuntu release this affects.

mutt is version 1.5.20-4ubuntu.

Seems to be present in final release as well.

$ dpkg -l mutt
Desejado=Ignorar/Instalar/Remover/Eliminar/Manter
| Status=Não/Inst/Arquivos-Cfg/Descompactados/Configuração-Falhou/Instalação-Quebrada/Aguardar-Gatilhos/Gatilhos-Pendentes
|/ Err?=(none)/Reinst-necessaria (Status,Err: maiúsculas=inválidas)
||/ Nome Versão Descrição
+++-==============-==============-============================================
ii mutt 1.5.20-4ubuntu text-based mailreader supporting MIME, GPG,

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.)

So I think the problem I'm seeing is probably a regression from http://dev.mutt.org/trac/changeset/b080ae086a62 , which explicitly sets the atime if a mailbox still has new messages in it. (I guess I should get out of the habit of force-write ($) and then exit-without-writing (x) to avoid having messages changed from new to old when I haven't caught up on the list of new things.) Do you also have messages marked as new in the mailboxes for which this is a problem?

This is possible related to http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=533439 and http://dev.mutt.org/trac/ticket/3271 , though I'm not sure.

I see this even when closing out folders with c (change to another folder); mutt will still prompt me saying the folder I just left has new mail. It's not just $ and x.

It's an upstream problem and apparently was intentional.
There's a little discussion and an acknowledgement that they broke a lot of people's workflow at http://dev.mutt.org/trac/wiki/NewMailHandling
Someone posted a patch at http://dev.mutt.org/trac/ticket/3271#comment:18
but the current resolution is basically that yes, it's broken now, "we're planning to rework the new mail handling".

For now it seems the only answer is to build a local copy of mutt with the patch, or use an older version.

Marking as confirmed and linked to upstream bug mentioned in comment 5.