I have the following settings in my muttrc file:-

    set alias_file=~/.mutt/aliases
    set arrow_cursor
    set assumed_charset="iso-8859-1"
    set confirmappend=no
    set delete=yes
    set editor=~/.mutt/bin/vimutt
    set folder=~/Mail/folder
    set folder_format="%N %-32.32f %d %6s"
    set index_format="%3C %Z %{%d-%b-%y} %-15.15L (%?l?%4l&%4c?) %s"
    set mail_check_recent=no
    set mark_old=no
    set mbox=~/Mail
    set mbox_type=mbox
    set nomove
    set nomarkers
    set query_command="getEvoAddress.py %s"
    set record=~/Mail/Tm/sentmail
    set reply_to=ask-yes
    set rfc2047_parameters=yes
    set save_empty=no
    set signature=~/.sig
    set spoolfile=~/Mail/In/inbox
    set status_format="-%r-Mutt: %f [Msgs:%?M?%M/?%m%?n? New:%n?%?o? 
Old:%o?%?d? De>
    set status_on_top=yes
    set timeout=15

I think the only really relevant ones to this problem are:-

    set mail_check_recent=no
    set mark_old=no


.... but the next-unread-mailbox command is *not* taking me to mailboxes
with unread mail.  If I navigate manually to these mailboxes there are
messages flagged with N.  So what's wrong?  Why isn't next-unread-mailbox
finding the new mail?

These are mailboxes listed in the 'mailboxes' command in my muttrc.

It's as if next-unread-mailbox is first doing the same sort of check
that 'c' does and *then* looking for N messages.  In my case 'c' won't
find new mail because access times have been changed by overnight
backups etc., next-unread-mailbox did seem to work yesterday (before the
backups ran).

-- 
Chris Green

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