I've had outlook 2003 for a few weeks and it was fine. I had shut off the junk mail filter immediately as I had my own spam filtering tools.
Recently, it has started deleting messages (from the server) once they have been read. Only some messages are deleted, not all of them. I haven't found a pattern to why some messages are deleted and others are not.
I did turn on the junk mail filter to see if it would catch the spams that got through my filter, but I turned that off.
Some online info suggested checking the current view to make sure it's set to show read messages. (Seems to apply more to pop).
These messages are not moved to the followup folder or any other folder than I can see.
I use Outlook 2003 set up as IMAP to a server running Imail.