>I recently made some major changes to a project I was working on - including
>removing some tables and adding some new ones. I went to into the database
>designer to remove some of the old tables and edit the referential
>integrety. I got a message saying that I need to run "Clean up Database"
>from the Database menu. Only problem is, its greyed out. Any ideas?

Do you have SET EXCLUSIVE OFF? If so, that's probably what it is.

(See Jay's answer for the right way to take care of this.)