Steven, I did some test in these days. I'm trying to tamper with the options, to better understand what is going on.
I found part of the problem (and now I understand it's not a problem, maybe): when I'm in ORGANIZE LIBRARY FILES, I find a couple of rows, one with MUSIC, one with AUDIOBOOKS. Well, I have no audiobooks in my collection, so that row is unchecked. BUT when I start the process, for example if I changed the Naming Template in the Music row, and I hit the PROCEED button, the software STILL CHECK THE LOCATIONS THAT FIND in the other unchecked rows (in my case, audiobook), and return me an error because in that row probably I had a wrong/old path.
This is annoying, also I can't remove useless rows "in excess".