It may help if you could provide a little more information such as the FileMaker versions you are using and which applications (is Pro or Server hosting the database?). Also, what is the behavior that you are experiencing? Do you click on a database and do not have access? Do you not see the database at all in the Open Remote window? Do you click on a database but it disappears/crashes? Can you open other databases without issue?
If you can see the database, I would start by verifying that you still have proper privileges to access the file. Will an Admin account work? Can you access the database if 'All Users' is selected for sharing? If you do not see the database file, verify that port 5003 is open on your machine. Also, if you can not see the database file can you see the server's ip address?
Hopefully the exact behavior of this issue can point us in the right direction for a proper resolution. Keep me posted.
I have the same problem. Installed FM Server 11 and see files in databases, however on the remore FM Pro, Open Remote, double click on the Server, it displays "no files"