Hmmm. May have made a very elementary mistake here. I put the files straight into the root folder.

Would it fix it if I just put all the folders into a "Flac Music" folder and Initialised/Updated on the Rockbox firmware?
Post Merge: August 04, 2011, 10:05:51 PM
Sorry for the double post.
I seem to have figured out the problem:
MusicBee saves the playlist file like this for example:
G:\Flac Music\Muse\2003 - Absolution\(05) [Muse] Stockholm Syndrome.flac
But when I use it's synchronise feature it transfers files like this:
K:\Flac Music\Muse\Absolution
That is, for some reason, it doesn't directly copy paste from my harddrive to the ipod, but rather uses it's own sorting method. By Album name saved on the IDtag.
Rather annoying...