How does Gnus decide to mark email as 'read'?

[Giorgos Keramidas]

I've been having on and off a problem with Gnus that makes it a bit hard
to track groups with new email.

I use fetchmail to pull email from various email accounts and save them
to `~/Mailbox'.  Then the following select methods to periodically pull
them into Gnus for reading and replying:

  (setq gnus-select-method '(nntp "news.sunsite.dk"))
  (setq gnus-secondary-select-methods '((nnml "")))

Most of the time things work fine, and I see new email messages in the
*Group* buffer.  But sometimes, Gnus pulls emails from `~/Mailbox' and
spools them into existing `nnml:mail.*' groups as ``already read''.

When this happens, typing `g' in the *Group* buffer shows no new mail.
Messages that I haven't really read have been saved in a group like
`nnml:mail.freebsd.arch' but I can only see them if I manually visit
each group with `C-u RET' and look for `O' marks like the last two
messages in the snippet below:

  E  2009-04-03: Kamlesh Patel        (  37) GSoC 2009 Project proposal Review
  E  2009-04-03: Sylvestre Gallon     (  66) +->
  E  2009-04-04: Ivan Voras           (  47) +->
  O  2009-04-05: Sujit K M            (  20) `->
  O  2009-04-05: Ivan Voras           (  34)   `->

How does Gnus decide that these are already `read' messages?  Is there
any way to fix this, sort of saving my nnml folder archive, blowing it
away and selectively restoring `nnml:mail.*' groups?

FWIW, I am using Gnus v5.13 in a relatively recent snapshot of CVS Emacs
23.0.92.1 (i386-unknown-freebsd8.0, GTK+ Version 2.14.7) of 2009-04-05.
But this has been happening on and off for a while, even with Emacs 22
so it may be something that is broken with my `nnml:mail.*' archive.