This occurs only if you encrypt via the button "Sign/Encrypt" in Kleopatra, when you start via the Explorer the selected files and folders are both encrypted.
After clicking "Sign/Encrypt" in Kleo, select some files and folders.
Note that only the names of the files and not the folders are listed in the field "filename" at the bottom.
If you proceed with "Open" only the files are added to the encrypted archive.
This is as intended, in Kleopatra you either encrypt files or folders (via File-> Sign/Encrypt Folder).
But this is a usability problem. Can we change this?
No. Windows has a file selection dialog where you can only select files and a folder selection dialog where you can only select folders. We cannot change Windows (and we will not use a non-native file dialog).
Could we then clarify this for the user somehow? Maybe both
a) add "Sign/Encrypt Folder" to the default menu bar - it would need an icon added for that, too
b) make it clear in the documentation
I am not sure how often I said this already. I documented this multiple times and spend days trying to find a way around this. So I tend to just scream "WONTFIX!"
But we talked about this yesterday. And yes I will try to somehow look for something to improve this. Since this was also reported by a customer, otherwise I would say that this issue exists only because Linux users are unused to the dialog.
I've added a footnote in the VSD user documentation regarding this difference as a very minimal measure and a reminder for support.