Sorry for the trouble. Someone else just reported this issue via email. And they’ve provided me with access to their site so I can troubleshoot. I’ll update you when I’ve found a fix. In the meantime, you can also edit MTs preferences via the General > Preferences option in the main Microthemer interface. That should work if your problem is exactly the same.
Just to let you know, I’ve released an update (184.108.40.206) which fixes the issue on the standalone preferences page. It also includes new transition properties, which were previously only available in the beta.