With the greatest respect in the world, my first recommendation to you would be to buy some good books on the subject and/or go to a short course devoted to equine reproduction. I say this because there are obvious inconsistencies in what you are reporting, and I suspect strongly that both you and your vet are in over your head. If you work at gaining the knowledge, that understanding will help everyone greatly - not the least of all your horses!
Due to the weather here we didn't even get the mares coming into season until April (it was snowing until end of march)
The weather doesn't play a part in the onset of seasonal cycling. Duration of light exposure does, but in fact there is not a high degree of light intensity needed to start the cycling, and the weather (short of darkness caused by Mt. St. Helens erupting again) will not have a significant enough impact to be noticeable.
vet said we should PG them we did so. They all came into season
If they were not cycling, they would not have come into season!!! See the article on prostaglandin use for more information on the use of this drug to cause estrus (and why it sometimes doesn't).
We could have put them on a box for 2 hours and take them to the University but it was decided that would do more harm than good.
Why? Assuming the horses were good to travel, and the transport safe, you probably would have been far better off to do that. There is no indication of a link between transport of healthy happy horses and a reduction of pregnancy.
All of the mares were covered once (one mare was covered twice) from 5-10 days after shot, (5 mares), the other 4 that were PG'd came into season squatting etc, but would not let the stallion mount - they were hand bred, but tried to kill everyone including the stud, but they were fully in season.
How do you know they were fully in season? One of the signs of a mare that is "fully in season" is that she will stand receptively for the stallion... The fact that they had received prostaglandin does not necessarily mean that they came into heat! (See the above article for details).
The same vet came out to u/s the mares (we have stocks) but he was worried about 'breaking his arm' he thus only got one mare done,
If the stocks were too high in the back, that is a serious consideration. If he was as inexperienced at palpation as you suggest, then there was also a risk to the mares, so perhaps the end decision was best for all!
whereby he saw 2 black perfect circles in the horn
If pregnancy checking "2 black perfect circles in the horn" would be suggestive of twins, cysts or fluid. Twins would be a big concern. If checking prior to/during the breeding cycle uterine fluid such as that would require treatment.
but then a slightly larger white round which he said was the egg which had been dropped 4 days prior
It would not be possible to give an indication of how many days prior the mare had ovulated unless a previous ultrasound had shown the presence of a follicle which had now been replaced by a CL. Note too, that one cannot see "an egg", which is microscopic, so if he really was thinking he saw an egg (oocyte), someone was sadly mistaken!
The other thing is his U/S is very old- could it be the white was an actual foetus just not far along enough to be seen by his old scanner???
Is the black circles actually foetuses?
It may be, and you may have twins. (As a technical point - up to about 35 days, they are termed "embryos". After 35 days, they become fetuses).
I really need some advice as I was thinking about boxing these mares to the Uni
Here's my advice: Take them to the University.
however what should I do with the four that wouldn't let me cover them?
Take them too.
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