Hi, this was reported by a few people, and I fixed it in the new 0.2.1 version I uploaded a few hours ago. Could you try the latest version and see if it's fixed?
Saving now works. What I'd still like to see is the option to freely swap the Start and B button (or the A button). That way, you could assign either the A or B button to the Crank and the Start to a button. The reason for this is Pokemon Pinball, which was controlled using the Start button on the Mini. However, that doesn't work well with the Crank.