I think a change was recently made to the library auto-organise function because when I opened up my settings and clicked Organisation, I had a ton of files that did not match my rules that had to be re-organised. The changes mostly seemed to have to do with capitalization.
Now, every time I click on the Organise button, there are about 15 files that need to be re-named. Mostly the change is just adding an _1 to the end of the filename for seemingly no reason. When I click Proceed, it doesn't actually re-name any files and when I open the list again, there is a different list of files for the same change.
This is my naming template: <Album Artist>\$IsNull(<Album>,,<Album>\)$IsNull(<Disc-Track #>,<Title>,<Disc-Track #>" "<Title>)