Thanks for your very promising plugin!
I created post types, then installed your plugin, then assigned relationships, however I'm finding that when I edit a CPT post I'm seeing autocomplete boxes, not checklists. Is the latter no longer your default?
I'll add your custom filter code but am wondering where the glitch is occurring - something I've done? something you've done? documentation needs updating? - and if there's a way to correct it in the admin interface without having to add custom code.