We're aware of an issue affecting FileMaker Server 13 on Yosemite OS X 10.0 Where we cannot open database files via the FileMaker Admin Console, and/or receive the license key conflict error below.
“Another copy of FileMaker Server (<ServerName> [<IPAddress>]) is already running with this license. This copy of FileMaker Server will not open any databases, but will allow updating the license key in the Admin Console.”
This error refers to a mismatch between the Computer Name, and the FileMaker Server name.
For how to fix, please see FileMaker's Knowledge Base article, here: http://help.filemaker.com/app/answers/detail/a_id/14127/