Before work this morning just before sunrise I went to take a look at the entrance of the hive, just to say good morning to the girls. Well as I was there I could hear a high pitched squeek, hard to describe,anyway is that the queen piping?

Also I looked in the hive sunday and the queen seems to be laying good ,I guess 2nd box up had a little capped brood but i saw quite alot of larve. alot of the capped brood was at different heights not uniformed height looked kinda strange, ??? The frames are frames from the brood chamber we extracted and we didnt get the caps cut off very square ,the brood chamber was honey bound last year so i extracted and put them back in last year . could my damage to the comb cause this?? She hasnt layed in the lower box at all! it has alot of pollen and there is quite alot of uncapped honey but it seems that there alot of space for her to lay but she hasnt used any of it.
any suggestions from you wise people would be greatly appricated,
thanks Malcolm