Are the hidden directories a problem? Are they explicitly in the MediaBox library (as shown in the Folder Icon/Library Tab)? Using the MediaBox file browser, I didn't see how to explicitly add hidden directories (although I didn't try very hard). As an experiment, I added some directories
~/Test and ~/Test/.hidden
and some videos
~/Test/A.flv and ~/Test/.hidden/B.flv
When I added ~/Test/ to the MediaBox library and browsed my videos, A.flv showed up but B.flv did not. So I was wondering if the hidden directories could be the culprit here.