Replying to my own email. I wrote:
I'm running Centos 4.2 with kernel-2.6.9-22.0.2.106.unsupported and jfsutils-1.1.10-3.2 from the centosplus distribution, with a jfs partition for my maildir mail spool, accessed using the dovecot IMAP server. It seems that dovecot doesn't properly track new incoming email, apparently because the modification time on .../Maildir/new doesn't get updated when a new message is linked into it from .../Maildir/tmp.
It appears the problem is fixed in 2.6.15:
http://www.kernel.org/git/gitweb.cgi?p=linux/kernel/git/torvalds/linux-2.6.g...
Looks like a simple change, so I may well try backporting it to the current kernel myself when I can get organised enough.
Meantime a regular
"find /mail -type d -name new -print | xargs touch"
(euwww :) appears to do the trick.
James