When sending in support tickets, it is often very useful to attach screencaptures for us to look at. Sometimes the words you use aren't the words we'd use and the real issue can be unclear. A screencapture is indeed worth 1,000 words, in many cases. (more)
When strange things happen on a Mac, like settings not being stored, license codes not being accepted, or DEVONthink databases behaving unexpectedly, file permissions could be the cause. UNIX permissions and Access Control Lists (ACLs) define what the logged-in user and the applications opened by her can do with items in the file system. If you want to learn more about permissions, have a look at Take Control's new ebook Take Control of Permissions in Snow Leopard which explains this geeky subject in easy language and hands-on manner.
Sometimes, file permissions go bad and leave 'locked' or 'used' files behind. If this happens to your DEVONthink Pro database, the application will continue to claim that the database is in use. If you are savvy with file permissions, use either the Finder's Info panel or the Terminal to correct them. Make sure to adjust the permissions of all files in the package. A trick that also seems to work in some cases is to duplicate the database in the Finder and open the copy instead.