There is a work around for such behaviour. The behaviour you are getting I believe may be due to carnac but I could be wrong.
Carnac is made to import media and fill in empty database fields using available information but sometimes it can be hit or miss.
More reading on Carnac here
https://wiki.jriver.com/index.php/CarnacBut anyway, I've had the same issues but there's an easy workaround using auto import. If your movies and shows are in separate folders you can configure the auto import to apply certain tags upon import. Just make sure you have separate entries in Auto-Import for each your movies and shows folders. Rather than having one import folder being the root folder of your media.
Go to Tools > Import > Configure Auto-Import.
Do for each folder i.e. the movies folder.
Select it, press edit and in the new window you'll see at the bottom "Apply these tags (optional)"
Just add Media Sub Type: Movie and click ok and now all new imported files within that folder will have the Media Sub Type set correctly always
Hope that helps