The current documentation for FMServer regarding the location of files that can be hosted needs a bit more clarification. The clarification is that the server will only recognize files that are stored in the specified folder and in one folder below that. So you can't create a sub-directory depth of more than 1 folder.
Here's the current FMS 15 help document:
And for FMS 16:
Here's the KB article that does the clarification: