Ok so where I was getting confused was. I have a group promotion called competition voting, that all registered members go into once they've been a member for two weeks. Which is why "registered" was unticked in secondary user groups, because "competition voting" was ticked. So it wouldn't let me re-add them to "registered" in secondary voting anyway. If I added it and saved it just removed it again.
I think it's sorted now anyway! Cheers.