Sub-folder structure not re-created

This is tricky.
The easy solution is just to organize with the complete scheme: artist/album/cd/title, with a custom filename pattern.

Another way is by using the automatic folder reproduction, what you were using with 1.4.4.

When SoundConverter starts, it tries to reproduce your folder organization.
For this to work, you have to pass multiple files/folders.

It's really simple: first: disable "create subfolders".
then select your destination folder (music.MP£ in your case), the same you are already using.

The catch is now: SoundConverter uses the common root of all files passed as a base folder.
so if you pass:
path/artist1/album1 and path/artist1/album2, the common path is path/artist1/
In your case, you must pass either multiple artists, or add another file to the root of you input path, just to trick
SoundConverter to recognize "music.FLAC/" as the common root folder.

so either:
path/artist1/album1 and path/artist2/album2, -> common path is path/, want you want
if you are converting just one album:
path/artist1/album1 and path/dummyfile.mp3, -> common path is path/, want you want

This way, your organization is be preserved.

I hope this is clear!