So are you talking about the little screen that comes up at the bottom right from Messenger that tells you you have new mail, etc? If so I think the alerts option is the one to look at as those are pretty normal and not a trojan or spyware.
Another place to look is in Outlook Express look under tools, options, general tab there's a check box for starting messenger. It will also start if the contacts pane is on in Outlook Express. For Outlook 2002 it will be under tools, options, other tab, there's a check box there at the bottom...
One thing you might try is renaming or deleting all *.rhc files (they'll look something like MSIN5006.RHC in the Outlook folder). It will download all messages on the server again but it'll reset the list. Might be worth a shot, those are the files that keep track of what's been downloaded...
What version of Outlook are we talking here? They handle things a little differently depending on version. Have you tried turning off the option to leave all on server then turning it back on again. There are some entries you could possibly rename as far as the list Outlook keeps but again...
On a quick note, while it will get all your folders it will not get any rules or account setup info. Account info you'd have to just know, rules you can export on their own if they are important. To do that you would go to tools, rules wizard, options, you can export from there. Just thought...
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