See:

https://bugs.kde.org/show_bug.cgi?id=367641

For some reason, every click on one of the options such as healing causes an empty settings document to be read which resets the option. I reverted

commit 139f5a61e1c139b1c9e91460fdfbc971e972813d
Author: Dmitry Kazakov <dimula73@gmail.com>
Date: Thu Jul 28 13:16:41 2016 +0300

Added HUD properties to the Clone brush

And that "fixed" the issue.