When you encrypt a folder in the X: drive, Boxcryptor creates a new folder with the same name plus "_encrypted", encrypts the files and stores them in the "_encrypted" folder.
If everything went fine, the original folder is deleted so that you only have the "_encrypted" folder.
If there was a problem, the original folder is _not_ deleted - for example when a file in the original folder could not be read because it is already opened by another application.
I'd recommend to delete the "_encrypted" folder, make sure that no other application is accessing the files in the original folder and re-try the encryption process. At the end you should only have the "_encrypted" folder.
PS: Also check if you're using the latest version which you can download here: https://www.boxcryptor.com/en/download