If you install FileMaker Server web publishing services on an OS X Server machine it takes over the default http and https ports, 80 and 443 respectively. What this means is that you cannot have FileMaker Server web publishing and built in OS X Server web services (ie. - Profile Manager) on the same machine. Even if you then uninstall Filemaker web services, you may find that it holds on to the ports and you will not be able to load default OS X Server web pages. You can usually check this by going to Activity Monitor, and search for httpd. You may see multiple services owned by fmserver, which is the indication that FileMaker web services has taken over.
You can manually unload the processes but it will load itself up at next restart. So try going to /Library/LaunchDaemons and look for com.filemaker.httpd.graceful.plist , com.filemaker.httpd.start.plist , and com.filemaker.httpd.stop.plist. Remove them and restart. Always back up these files first as a precaution. I would also recommend stopping and starting OS X Server web services and/or Profile Manager and clearing your browser cache.