Can a rooster cause ovarian cysts in hens?

I know it seems crazy but one by one it seems my flock (down to 10 hens) is getting ovarian cysts and ascites. It seems to have started around the time my rooster became mating age. I had a necropsy done on the last one that passed and all they found were cysts in the ovaries and ascites. I lost one a week before that and another a month ago with the same symptoms. I have another one that is starting to show the same symptoms. All of the hens are between 1.5 - 2 years old and all different breeds. There was nothing contagious found in the necropsy results. Could my luck just really be that bad? It seems like there must be something causing this.

The symptoms have been: water belly, diarrhea, not laying, not eating/drinking, shivering. They end up starving because they stop eating/drinking. I wormed them in December. They seemed to be cocci type symptoms so I treated with Corid but the necropsy showed no cocci signs and neither did a fecal sample I had done prior to the necropsy. I give them fermented organic feed for breakfast and a mix of organic pellets and scratch and peck for dinner. I've also started giving them vitamins in their water. It's been a really wet/rainy winter and they frequently drink the rain water in the run which I'm sure is not good for them but not sure if that could cause the cysts and ascites.

I can't imagine how the rooster could cause it.

Once you have examined every possible cause this will not be a mystery. Here are my thoughts:
1) Have you introduced any birds to the flock?
Birds are vulnerable to diseases and one sick bird can infect the others.
2) Where did you get your birds?
3) Do you have any toxins in your back yard soil?
4) Are your birds inbred?
I had a stray cat who had one litter, where there were 5 females and one tom. We spayed her, and my Vet spayed 4 others of her kittens and she AND her daughters ALL had crossed ovaries, which my Vet said was caused by HER parents being from the same litter.
5) Where do you get your feed?
6) How do you store your feed?
7) Are you sure that your fermentation was safe for them? Fermenting can fail.
"Making fermented feed:
You need a non-metal container. Acids from fermentation can react with metal and leave bad things in your chickens’ dinner, so use plastic, glass or lead-free ceramic crocks. Be sure to get a BIGGER container than you think you will need."
http://www.theartofdoingstuff.com/how-to-ferment-chicken-feed-bigger-eggs-healthier-chickens/
Unless your rooster has an infectious disease I can't see him causing your problem.
Hope you solve this soon! Nothing dampens your chicken keeping spirits more than dying birds.

1) Have you introduced any birds to the flock? Birds are vulnerable to diseases and one sick bird can infect the others.
No, none recently.
2) Where did you get your birds?
The oldest ones (2 yrs old) came with the house. I don't know where the previous owners got them from. The next batch I got as one day old chicks from a local company that gets their chicks from various breeders and the last set I got as hatching eggs and let a broody hatch them out. None from the youngest batch have shown any signs of illness and are all laying fine.
3) Do you have any toxins in your back yard soil? No toxins that I'm aware of.
I use organic gardening principles and don't treat the lawn or garden with any chemicals
4) Are your birds inbred?
I had a stray cat who had one litter, where there were 5 females and one tom. We spayed her, and my Vet spayed 4 others of her kittens and she AND her daughters ALL had crossed ovaries, which my Vet said was caused by HER parents being from the same litter.
Not that I'm aware of. I'm not sure how the breeders and hatcheries I got the chickens from breed them though.
5) Where do you get your feed?
local store (I use Organic Payback and Organic Conway brands)
6) How do you store your feed?
feed is stored indoors in Ikea containers
7) Are you sure that your fermentation was safe for them? Fermenting can fail.
I don't think there's any problem with the fermentation. It doesn't have a foul order and I use a plastic container. I use most of the feed in the morning and add additional water and feed to some of the already fermented feed to make a new batch every day.

The only causes I've found for cysts is genetics, growth hormones, old age and possibly infectious bronchitis. I don't think any of those apply. 1.5-2 years old doesn't seem that old to me. 2 of the 3 that have passed were from the original flock that came with the house and they've had no illnesses for the year and a half that I've lived there. The sicknesses started a couple of months ago and start with diarrhea. I thought the necropsy would show something but nothing came up other than the ovarian cysts and ascites so not sure what it could be. Not sure if there's any specific tests I should ask them to do on the next one if I send for a necropsy. It's only $25 for a necropsy but there are additional tests they can do if they see something they need to confirm.