In the topic subject, you mentioned that you can't get Auto-Tag by track (infer and update tags from filenames) to behave...where is it failing?
When you use something like <Artist> - <Album>\Audio Files\<Artist> - <Track#> - <Title>, don't you get the results that you're expecting when you hit preview?
And inside your album folders, are all your tracks contained in an "Audio Files" folder? If so, then the above should work well I think.