Is this a production server? If it isn't you might be best trying a fresh install. If it is a production server then follow these steps:
1. Backup your CRM database.
2. Install CRM onto a new clean server (make sure all Windows updates are installed)
3. Restore the database backup to the new server
4. Redeploy the CRM database as a new CRM organization by using the CRM deployment wizard.
For more information use the CRM 2011 Implementation Guide (here: www.microsoft.com/.../details.aspx)
Also before you do this check you have not got scripts that are not Rollup 12 compatibile.