Yep if you win the special puppy class regardless if it is over 12 months it will be best puppy dog/bitch then it will challenge for best puppy in breed.

I'm afraid the secretary was wrong and also acting totally incorrectly. Once the judge has declared best puppy, given you the rosette then noone can change that except for the KC. Even if the lady who had come first complained and the secretary said she was Best Puppy nothing could be done on the day of the show. The KC have to be notified by the club and they decide what happens. Now the owner who got first was fine about it and didn't request it be taken further. However if the KC looked though and checked the results fully (which I doubt they would do) they can investigate themselves and take best puppy off you and reinstate the original winner. So the secretary on the day got two things wrong. Firstly she has no power to make those decisions once the award has been given and secondly. It clearly says in the schedule puppy is 6 months to not exceeding 12 months so if a dog is 12 months on the day of a show (open show) then it is still a puppy as it does not exceed those 12 months.
As leospride said earlier Champ shows are a different matter as they are run over a number of days.
I had it a couple of years ago. My boy was 9 months old on the 5th but the show started on the third and the rules of the champ show goes on ages on the first day of the show. Therefore he could of gone in Minor Puppy as he did not exceed 9 months on the first day of the show. I however did put him puppy as I wasn't totally clear on that point and got confused on the day when his litter brother was in minor puppy.
Anyway enjoy your win. At the end of the day you've got a lovely pup, you were awarded best puppy and it wasn't your fault that the steward, judge and secretary cocked up. Fraid it happens. You learn from these things.
Hopefully RIO might come on a tell you about her cock LOL