As a 'general' rule: Install FileMaker files on the FileMaker-Server using the built-in functions. Don't copy files using commands from the Operating System. Reason: Permissions... (especially on OSX)
When errors occur while installing FileMaker files, there is something else to be fixed
Ok thanks, so it looks like I'm probably going to be doing a fresh install of Windows and FM Server 13 to see if that fixes it...
Before you do all that, maybe see if the connection failed problem is network related.
From past experience diagnosing problems with web servers is painful, I did a clean install of Windows 7 and FM Server 13 and it's all working now.
Thanks for the help.