I believe that the black folders indicate that there's an album in that directory - yellow folders do not. From my quick testing, it appears that the presence or absence of a thumbs subdirectory is how it tells the difference, but I'm just guessing.
No, in my case all black and yellow folders do contain albums. I see black folders only on the jalbum server, see AndreWolff.jalbum.net.PNG If I click on the + sign of a yellow folder, the folder becommes black.
On my other server I see only yellow folders, see www.andrewolff.nl.PNG and they stay yellow if I click the + sign.