I'm also having a problem with folders, and subfolders changes not getting picked up by FIM. I tested it by making the folder/subfolder mask recursive, and created and deleted some folders. I had also applied create and delete options for files, and when I created and deleted files, those were accurately reported. Even in subfolders, which were new, however the creation of the subfolder was not listed in Solarwinds.
It looks like it's the "folder" check above which isn't getting recognized.