There is a utility "UpdateMedia" that runs in the background and always adds your media files to a sqldatabase. You can confirm this in pluto admin by going to files & media, media files sync. If the files have a check mark they're in the database. The log is /var/log/pluto/UpdateMedia.log, and the files go into teh pluto_media database, File table.
The file browser has changed, both for UI1 and UI2. It used to be that it was doing a directory listing. This meant you had no way to do sort or filter.
Now with .43 it uses the database. This should be much better. Now you can sort by title, performer, etc. Also you no longer have to remember what is where. If you bring up music, for example, and touch the shortcut for 'Jennifer Lopez' you get all her songs, no matter where they may be scattered around the house.
If you choose the options buttons and sort by filename, the results should then be the same as they were with .42, meaning you see a directory tree and can drill down like before. The layout is still different because we made the cover art bigger; it was very small before and hard to read. but the content should be the same.
It should be easier for the kids to find what they want, I think, because now if they want 'Barney', they just "B", whereas before they needed to know which drive/directory it was on and drill down. If it's not working, that probably means UpdateMedia didn't add the media files to the database somehow. Please check the log and the database.
Let me know if you don't find this to be the case.