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And I have 3 neutered boys and know nothing about breeding but I do hope someone who has experience of this may be able to help you,

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Selina, Simba, Jinx and Rufus

I have heard of pregnant girls calling, but you need to get them seen by a vet and if still unsure a scan to make sure first. You could just wait and see but if you want to know for certain and not wait then a vet visit is necessary.
As he is "proven" having sired the kittens from the full sister and aunt, then you need to look at your two girls. Are they of good weight and size?
Are they healthy?Are your girls fertile?
Being mother and daughter is there some genetic component stopping them from maximum fertility?
Do they have a discharge? Is there some infective problem altering their fertility? Did they perhaps visit him too early or too late in the cycle? Are they calling regularly?
Are they letting him do his job?
Are they letting him mate? Have you seen them mating?
Do you leave them to it or do you observe? How long was he in with them in total?
Is he lower in the pecking order and they are bullying him?
Is he perhaps sub fertile?
Did he get the two pregnant before or after he was with your two non- pregnant girls?
If they were after, then perhaps he needs checked out "down below" in case he perhaps has injured himself or has an infection.

Thank you all so much for your replies, I hope I didnt sound sarcatic, it was not meant to be.

It looks like I still have a lot to learn about this mating game, and I thank you Junglerose for your input.

As he is "proven" having sired the kittens from the full sister and aunt, then you need to look at your two girls. Are they of good weight and size?
He has mated 3 cats and has had live kittens but not big litters on 2 in each, so I am sure he was fertile

Are they healthy?Are your girls fertile?
One of the cats is a maiden so not sure about her fertility but her mother has already had two litters, one of them by him. She is the one who has returned to call for the 2nd time. They are both very healthy and in excellent condition.Being mother and daughter is there some genetic component stopping them from maximum fertility?

Do they have a discharge? Is there some infective problem altering their fertility? Did they perhaps visit him too early or too late in the cycle? Are they calling regularly?
They is no discharge or infection and they seem to be calling regularly

Are they letting him mate? Have you seen them mating?
I am not sure they are letting him do the job as I havnt seen him do it. I have seen him mount them though.
Do you leave them to it or do you observe?
I do try to observe but they just dont seem to get on with it whilst I am there.
How long was he in with them in total?
I have tried leaving them with him all the time and taking them out.

Is he lower in the pecking order and they are bullying him?
He is a very shy cat so that could be a problem.

Is he perhaps sub fertile?
Did he get the two pregnant before or after he was with your two non- pregnant girls?
Before

If they were after, then perhaps he needs checked out "down below" in case he perhaps has injured himself or has an infection.

I was thinking it could be the environment. I have moved him as he was a very shy nervous cat when we first got him and I wanted him to get used to lots of goings on.

However when he mated previously (accept for one cat which I am praying is in kit) he was in a more secluded pen. So perhaps, as you say he is shy, so I will move him back to the other pen for his mating duties.

Although I havn't seen him mate I have noticed that one of the queens has the tell tale marks on the back of her neck, so fingers crossed.

Again thanks for your input. xx