As an owner of four grown Pekins I hope I can help you out here. My two Pekin females didn't go broody until this summer and they were a year old around june. It may be to early for your drake to start fertilizing the eggs anyways. If the eggs are strewn around the coop and not in one 'nest' then she will not sit on them. One of our Pekins lays in different spots every time and has never gone broody. The other goes outside and makes herself a little nest and lays there. Your duck will pick a spot and stay there if she decides to go broody, you'll notice because even during the day she won't move. The drake will also 'stand guard' over her. They may become protective and the drake may try to chase you off to protect his female and eggs.
I don't think she'll go broody anytime soon, she may but from experience it's pretty unlikely. It takes awhile for them to figure out how to be responsible. Even now my broody Pekin will forget about her eggs for a few hours or days- plus she made her nest outside which she doesn't have access to at night.
As for the different sized eggs, I'd say it's completely normal. We get eggs that don't fit in the egg carton but the Pekin is a very heavy breed. The majority of the time our eggs are double yolks. I'd crack a few and see what's going on in there just to make sure they're healthy. Though as long as the shells are hard and they don't look abnormal on the outside then they're probably good. Just take them out of the coop so they don't go bad or get eaten by the ducks because that is a mess you don't want to deal with.
This post is already really long...
So I notice you say you only have two ducks which is a problem. The ratio for female to male in ducks is around four to one. This means you must have four females for every drake. If you don't the drake will overlay her as well as other health risks. This can be extremely fatal and it's unfair to the female. Lots of people don't know about this when they first get ducks but from experience it is a very real problem. Also since one of your ducks is a drake you obviously aren't feeding them laying feed so you need to supplement your laying female with oyster or egg shells to strengthen her egg's shells.
I hope you found all of this helpful!
It was very helpful and interesting. I'm constantly researching and trying to learn about them. I did have 2 females but one went missing last week and she has yet to return. I have a large 4 acres pond and my ducks free range during the day but at night I lock them in their pen. My husband and I searched for her and any remains or struggle and found nothing. We do have large snappers in our pond which we are in the process of removing. My neighbor asked if a snapper got her but I didn't know if a snapping turtle could get a large duck. I know they will eat ducklings. My other two have been staying clear of the pond for the most part since she has gone and I put their baby pool near there pen/barn. When will her eggs be fertile!? Can I incubate them to hatch them in hopes to up my male to female ratio? I raised the ducks I have now from when they were just a few days old.I love them to pieces and I certainly don't want to cause my lone female any harm or stress.
