I just need to do one more step than I previously had to and click on the not recognised menu at the top of the scan results, which is same as notepad
Yes, you have to check the "not recognized" tab to see if you can rename the file to make the association work.
The notepad text is just a final report that comes handy after the scanning is finished. Now you can browse the database to find out what went wrong, if the movie is really missing or if there was a problem with the title or the year.
If the movie is in the database, it's possible to associate it manually by clicking the "play" icon. In some very rare occasions (2 movies with the same title and the same year and the one you own is the least popular), the manual association is the only thing that will work.