When I added two local folders to the Boxcryptor Drive, the only option that appears when I right-click on the folder is "Settings". There is no Encrypt option so I can't choose to encrypt the entire folder at once.
If I go into the folder, I can choose each individual file, one-by-one, and Encrypt. The option to right-click->encrypt then appears.
If I highlight all the files in the folder, there is no Boxcryptor feature when I right-click.
I had no problems encrypting right-clicking on the entire contents of a Microsoft OneDrive Folder, though.