Sorry I've found something else weird. The plugin works absolutely fine on the staging version of the website and plugins across the board are identical (pretty much)... the ones related to Mail Poet and Gravity Forms are anyway. On our production site however its acting strange.
So this is the thing. In Gravity Forms... Editing a Form. Adding a Mail Poet field. I have several lists. I check 5 of them... only 3 are saved. And always the same 3... See screen grab
Any thoughts? ... I'm going to guess you cant replicate it though.