Do you have your movies in individual folders? It may just be that you have a couple of movies that have subfolders like "subtitles" folder for instance. Cause if you are just judging this by what folders MC is scraping down the bottom this may be the case.
For me MC scrapes 399 folders but i only have 385 movies thats cause 14 of my movies have subfolders containing a folder called "subs"
Also if you go to file explorer and click properties on your movie folder. That will tell you how many folders and sub folders is in there is well.
2 double check i just count the folders in my movies directory my self. another way to do it would be to generate a .txt file of your movies folder using MSDOS then check them off
Use this DOS command in your movies folder to tell you which two movies have sub/folders
dir /b /s /ad > list.txt
This will create a txt file in your movies folder listing all you folders and sub folders. Just open it up and the subfolders will be the last ones listed. you could also just drop the >list.txt part and then it won't create a txt file and it will be just displayed on the screen, again folders containg subfolders should be the last 2.
Hope this Helps