I've been trying out the plugin the past couple of days. I like the UI and the accessibility of the crop thumbnail functionality (basically, its everywhere!).
I've only been trying it out on a bunch of my posts, but after I've modified the thumbnails on 3 or 4 posts, then it seems these get reset after I do 5 or 6 posts. I've redone those first 4 or so twice now, but have to give up.
My case may be unusual as I have 8 thumbnail sizes and 11 content types (according to your lists in the settings, and this does seem right). Perhaps because of this scaling issue there's something going wrong?
What information would you like to help you investigate this issue further?