Hello Ard Jan,
Include Subfolders:
You can encrypt a folder by using Secured Folders option. After that if you create a subfolder, it won’t re-encrypt the files of subfolder.
We can include the sub-folder by enabling the feature from the AxCrypt app menu File | Options | Include Subfolders. By default Include Subfolders will be disabled. So Sub-folders are not encrypted without enabling this feature.
Please check once again enabled the option “include subfolder” or not.
If the above doesn’t help, please provide more information about the issue and some screenshots and write a mail to support@axcrypt.net.