Quick update for anybody who may be interested or may want to help..
If I take away ‘showposts=4’ from the homepage loop it seems to solve it.. I can make a new post to the portfolio post type and my 4 featured/checked projects remain intact.. but I would quite like to keep ‘showposts=4’ in my loop because now if you check more than 4 posts you have unwanted posts stacking up on the homepage..
I did test that, mate, but the loop then only pulled out 3 of my 4 checked posts which is strange.
I’m sure it is something to do with the loop, though, because my code for the backend is working just fine – the checkbox values are properly stored in the db when you set the posts as featured – but the 4th featured post loses its value whenever I post a new portfolio item. Absolutely racking my brains this one.