...I think I just got an idea what is going on: It looks like windows/musicbee doesn't like some of the file names in my music folder. Windows just ignores these folders (shows them as locked and empty), but the the musicbee library scanner seems to get stuck on them.
I run a dual boot system with Ubuntu as my main system and windows as a play-box, so I never really noticed it. Anyhow, I just excluded some of the music artist folders that seemed to be troublesome (for example "Adult.", "Ascii.Disko", anything with an apostrophe) and now musicbee is happily importing the rest.
Looks like I am going to have a somewhat smaller library under windows.
So thanks guys for your help and friendly advice. Cheers!