Thank you for the post.
Did you download and run the update or the full installer for FileMaker Server 12v2?
When upgrading on 10.8, download and run the FileMaker Server 12.0v2 full installer software. Do not use the Updater. If you used the full installer, let me know and we will discuss additional troubleshooting steps.
For more information and to access the full installer download refer to Knowledge Base article 11044:
Thanks for the heads up TSFalcon, I'm trying this now. If you can alter the KB article it says the version of the installer is 12.01x when the link points to 12v2 - it's counter-intuitive and this may help others.
I'll update this thread with progress - seriously though, thank you!