Nu har jag hittat en lösning på problemet och kan äntligen slappna av. Kör en ren copy/paste ifall någon skulle få liknande problem:
I found a solution.
On some Macs Mail doesn't run the indexing after Lion has been installed. This behavior causes Mail to don't show the unread messages count right next to mailboxes AND it causes Mail to have a wrong count at the badge of Mails icon in the dock! (as mentioned in this thread: Unread mail count not correct with IMAP - MacRumors Forums)
The solution for this is:
1. Quit Mail if it’s open.
2. In ~/Library/Mail/V2/MailData, delete any file that begins with “Envelope Index,” such as Envelope Index or Envelope Index-shm.
Your home Library folder is hidden by default. To display it, choose Finder > “Go to Folder” and then enter “~/Library.”
3. Open Mail.
Mail creates new Envelope Index files. This process may take a few minutes, depending on how many messages Mail is reindexing.
(Found at: https://discussions.apple.com/message/15667297#15667297)
And you're done.