do you have sharepoint running on the server or anything else that may affect the standard IIS config?
Nope. Nothing like that. Just a vanilla IIS config.
Here's the windows component config for IIS.
And the WWW Service config.
All looks fine.
I know this sounds like a standard response, however I would recommend a full reinstall of FM server. Close files using admin console and then Backup first of course.
Once you have removed FM server, run CCleaner to remove any left over reg keys or temp files. If there are any Filemaker server folders left in program files then remove, or install fresh install of FM server to a different directory.
Install FM Server fresh, re-configure and run the WPE using the filemaker sample files. Test IWP/WPE using sample files.
Load each of your IWP/WPE enabled databases and test to rule out a databse config issue. That should at least point to the culprit.
Seems like Filemaker have recognised some of these issues, but when this will lead to a server update or patch is anyones guess.
I will be uninstalling FM Server and re-installing it this weekend. I will report back my findings after that.