Turns out the problem was that the cd ripping program was not encoding the files correctly. That has been fixed and it all works fine…. well…. almost
The second problem remains: If a file is renamed/moved he database is not updated with the new path, so it still shows up but will not play. I have to remove the file from the mt-daapd folder, update db, and replace it before the file will work. A very silly problem. (see http://forums.fireflymediaserver.org/viewtopic.php?p=8748)
As for the version thing, I am _very_ newbie to linux, and am running ubuntu. Whichever version I have was the only version I could find with a .deb package. If anyone has the time or inclination to explain how to automate updates to nightly builds, please do so.