Files will not be stored in the temporary folder, if you decrypt them. However, if you open the encrypted file via AxCrypt, it has to be decrypted and temporarily stored somewhere – and that’s the location you’re seeing. When you sign out of AxCrypt, or use the red “broom” icon to clean, or in many cases when you exit the application the temporary copies will be deleted.
This is no different from how AxCrypt has always worked, with the slight modification that sometimes you do need to use the red “broom” icon. This change was forced because of other problems with keeping track of when to re-encrypt and wipe the temporaries in AxCrypt version 1.