This topic has gotten somewhat muddy, so I'm going to rehash it here for clarity, hope no one minds:
The guy has:
Microsoft Messenger IM client.
MSN Messenger IM client.
(Windows Messenger alerter service is not involved in this problem).
His problem:
Both Microsoft Messenger IM client AND MSN Messenger IM client are loading at startup, fighting to see who's gonna log him in, even though he has set Microsoft Messenger IM client to not load at startup, and to never run.
That's the issue he's having.
So, I see at least a few possibilities: He somehow ended up with multiple entries for MSMSGS.EXE in his registry/MSCONFIG startup list, or he has a copy of Messenger in his Startup folder.
If the former is true, he can simply open msconfig and remove the check in front of any entry for msmsgs.exe. If the latter is true, he can delete the copy from his Startup folder.
If neither of these apply, first, what the heck is making it run? lol
Second: I'd try renaming msmsgs.exe, and seeing if MSN Messenger IM client still runs. If it does, he's golden. If it doesn't, I'm mystified.
Hope that clears this one up a bit.