strange...
Have you also looked at the (same) registry keys in HKEY_LOCAL_MACHINE?
Oh, do all that resetting when Messenger is not running, just to make sure...
Btw, the linked post in my previous post talks about Plus! adding the total unread mails to the Windows unread mails number. This is for MSN Messenger 6 and below, in Plus Live you have a preference option for that: Plus! > Preferences > General > E-Mail Accounts > Update the unread e-mail count in my Windows account.
Have you tried disabling that? (although I have a feeling this wont solve it).
What you also could try (out of desperation
) is moving all your mails from your inbox to another folder:
1) close Messenger completely
2) open hotmail
3) create a new folder
4) move all inbox emails to the new folder
5) click on sign out in hotmail and close the browser
6) reset all those registry keys again (both in HKCU and HKLM)
7) restart Messenger
8) check if the count is correct now, after recieving new email. If so (lets hope it is) put all the mails you moved before back to the inbox and check again...
other than that, I'm currently clueless...
/ 
