(2nd year beekeeper...)

Ok, my single hive died out at the end of March 2013. I replaced it with a nuc in early May (mostly Carni survivor stock bees - with dark brown queen) After 1 month, the hive was doing very well so I bought a full (dark) Carni queen in early June and did a textbook split from my new hive.

Three frames of brood and shook 2 frames into the new split, (made sure old queen was still in 1st hive and NO QUEEN CELLS ANYWHERE TO BE FOUND IN EITHER HIVE), left new hive queen-less for 24hrs, placed new queen between frames in her box for 3 days, then removed cork and carefully stuck toothpick through the candy. Two days later, I observed the new "dark" Carni queen walking around the frames like royalty.

Here is where it gets strange, 2 weeks go by, I can't find the new queen after multiple inspections, and lo-and-behold, I see this smallish tanned/brown queen walking around like she owned the place, no dark Carni queen anywhere. The new hive now has very little brood (about 1/2 frame worth). I thoroughly inspected ALL frames, old and new hive, without a doubt, there were no queen cells at any time from when I got the nuc in early May until now (June 27).

Some conclusions I can come up with:
1) I shook a daughter "queen" into the new hive without realizing it, which seems far fetched...
If this is true, then would the hive appeared to have accepted the new "dark Carniolan" queen if there was a current queen in there? After the first 24 hours mentioned above, when I went to place the new queen in the hive for the first time, there was a distinctive queen-less "roar".

2) Not sure why new queen is smallish (like 125% of worker with uniform tan abdomen), maybe she's not mated yet??

My goal was to add some genetic diversity to my hives, but it looks like I wasted $45 on the new Carni Queen.
I'm hoping someone might have some insight into what might be going on here... any and all thoughts are welcome.