If making this work with Preserve Folders and Filenames is getting too involved, I can switch to a manual directory structure.
It works fine for me using your sync settings. I believe you have auto-organise enabled for your library. The way it works is the auto-organise root path is used to get the relative path for each music file eg.
auto-organise template=C:\MusicBee\Music\<artist>\<album>\<disc-track#> - <title>
file=C:\MusicBee\Music\Dessa\A Badly Broken Code\02 - Poor Atlas.mp3
relative path=Dessa\A Badly Broken Code\02 - Poor Atlas.mp3
dest folder on device=MusicBee\Music\*.*
final destination path=MusicBee\Music\Dessa\A Badly Broken Code\02 - Poor Atlas.mp3
what could screw things up is if you have files in your library that dont comform to your naming template and not actually under C:\MusicBee\Music\ eg.
I think if this was the case MB would be using C:\MusicBee as the base for relative paths of all the synched files
final destination path=MusicBee\Music\Music\Dessa\A Badly Broken Code\02 - Poor Atlas.mp3
do you think that could be the case?
also one other possibility i could investigate, are you including files from playlists or a specific computer folder where the file is not in the library?
I tried both those possibilities and in both cases the sync behaved as expected so I am at a loss why its adding the extra Music into the path.
I can give you a debug version to see whats going on
perhaps you have some exceptions in your library naming template and define the root of your music library using:
C:\MusicBee\<some expression that evaluates to Music sometimes and other times something else> ?