The Rename tool will operate on files that it has imported into the database. Said differently, it doesn't try to rename files that are not imported nor belong to it. So if you want MC to manage those files, then you need to setup Import to also pull in the .txt and (not sure about) the .cue file. Not too many of us use .cue files so you'll have to search the forums here, or test it out.
You'll need to create a Rename Maintenance view, which will show all the relevant file types that are being managed by MC. When you want to Rename, go to that view, select the contents of the Album and perform the Rename.
Alternatively, you can do this outside of MC and MC will correct internal paths. You might find this easier in general if your music folders happen to contain files not imported by MC.
