Yeah - they wanted us to fullfil the "new" requirements whilst they were still using the "old" forms.
So they sent us away - didn't charge us again, though - and we came back with even more paperwork to show we'd been living together the entire 2 years and got the ILR no problem.
However, I know of someone who got sent away under pretty much the same circumstances, and she had to pay again.
It's all in who you get on the day, I guess. We'd actually been checked in by the guy who gave me my Fiancee Visa extension two years previous, so maybe that had something to do with it.