We have resolved this issue on Meta Box Users group on Facebook. Let me quote here in case anyone needed:
The CPT you created had some un-rendered labels. So I guess when you created the new CPT and you hit the Save button too fast (probably by press Enter), which makes the JS code hasn’t finished rendering all the labels and settings. Thus data saved is incorrect and makes WP doesn’t understand.
I tried to find that post ID (using the export tool of WP), and run a
wp_delete_post( ID ) to remove it. Everything goes back.