Hey guys,
Know this is an old thread but the same thing just happened to me. If my AVCHD content is in the same parent folder as other folders with media that I want to use, FCX totally ignores the directory structure and just feeds me a huge list of every piece of media in the parent directory….not just video, but stills and .pds as well.
The “fix” was to take the AVCHD files/directories OUT of the same parent directory where I have other content for this project, restart FCX and bing! Directory structure is back.