Possible solution for mp3's only.
Check this below, you could be saving APE in the options. I thought I had a bug until I realised that I had checked 'write APE' in the settings to help another forum member out:
[X] Genre tag from iTunes not updating
Read the full thread to see the problem I had. Yours sounds similar.
I'd recommend not changing filenames outside of iTunes as it searches files based on it's .xml file and if it cannot find it then a missing file error will show up.
I'd recommend instead to checkmark in the settings of iTunes > advanced tab
[x] keep iTunes media folder organized.
This way you organize tags only (minus the filename or course) in mp3tag and iTunes organises the files to folders and renames filenames based on their tags.