I did figure out one thing I had wrong. I had one single random mp3 in the root of an artist, and the Config program did not bother going into the rest of the subfolders with the other albums. Once I moved the single file into a Misc subfolder, it found the other bunch of albums.
I seem to have pushed enough buttons to get the Genre filter to work, however, they still do not appear in the loaded albums section of the config program. (Edit: I did the exact same thing after moving all the misc songs into Misc folders, pushed the same set of buttons, and now they appear. i'm confuzed.) (Edit to the edit:) I do th esame thing now, and I dont see the genres again. what a pain.)
I do seem to get multiple copies of the same album when filtering by genre, but not in the main menu.

I guess I'll play around more. My GF's files are all messy, so I am trying to clean a lot of stuff up for her.

I have a lot of files that were ripped from WMP, and havew WMA tags. I can't seem to get them to convert to ID3 tags, at least according to Mp3tag, and freebox keeps showing them as No Tag.