Okay, I think I figured it out. I had AmiKit X.app on the Accessibility list in the Security Settings, but it also had another AmiKit X listed there. I removed both of them, rebooted, reinstalled AmiKit X, and then it started working.
I figured it out when I went to run Flower Pot, which worked right away. It wanted me to add to the exception to the Accessibility list and that's when I noticed that AmiKit X was listed twice (once with the .app and I'm assuming the other was the actual executable within the .app).
So, it's working now!