It works great for everything excep maildir folders. At 1st I thought the the windows box was showing timestamps with second precesion whereas the BSD box was just showing minute precision, but that does not now appear to be the case. I tried the sync using file size instead of modification time.
My latest theory is that the mail messages in maildir have a ":" in them on the BSD side, but have "%3A" on the Windows side. So these files always show up as different, and are deleted from the windows box and then downloaded again from the BSD box.
Does this sound plausible, and is there a fix?