For some time now I have been struggling with my Outlook 2007 not shutting down properly. This usually manifests itself as the “outlook didn’t shutdown properly" message when the computer restarts or the inability to access my CRM customise entities page (as outlook is still running in the background).
I had (shame on me) assumed that my CRM 4.0 add in was the problem...
However - I've now found the guilty party - its Skype - check this blog post for more details and instructions how to fix it.