I successfully bred mice for about 3 years before getting rid of my whole colony. I was in college at the time and just didn't have the time to properly maintain them so my roommate didn't complain about the smell.

I ran 1.2, 1.3 colonies with a high rate of success. Where are you keeping the tanks for the mice? Are the females related? I've found anything over 1.3 causes problems. As far as I can tell from your post, the females are getting stressed out and eating the babies. The males make great caregivers, I saw my males helping care for the babies if I didn't get them out of the tank before the girls gave birth.

The best thing to do is to separate them into colonies of 1.3 or less. I kept my males in with the females for two weeks and then removed them to their own cage. Do you have more than one male mouse? Sometimes if the females smell a male mouse that is not the father of their babies they will get nervous and reabsorb their babies (if pregnant) or eat them if they have already given birth. The females should be related or raised with each other. Keep the same group of females together at all times, and I would suggest removing the males after two week so the females aren't constantly pregnant. If they are pregnant with another litter I have found they will wean the first litter to early or simply kill them if they feel there isn't enough food. They will also sometimes eat the babies if their tank is not clean enough.

When reintroducing the male for another breeding cycle, remove the females to a holding tank and clean the crap out of the tank everybody is going to live in. If the tank smells predominantly like the females, they will believe its their territory and harass and/or attack the male as an intruder. If the tank is mostly clean and the females have no babies, they will think it's neutral territory and after some squabbling accept the male. Also, rearrange the permanent furniture in the cage and clean out any hides you may use for the females.

Back to my first question, where are you keeping the tanks? If there is too much traffic in the location you are keeping the mice (you, other pets, even places there there is loud noise like close to the tv and/or speakers) that will make them nervous and cause them to occasionally eat the babies.

The last thing to do is, after you trim down the colony sizes, quietly observe the females when they have babies. Remove any females who seem to eat the babies for no reason. I had one trouble-maker in my first colony that was constantly getting into fights with the other girls, and later freaked out and ate the babies for no reason. She was retired early.

I want to stress keeping the girls in a given colony together throughout their entire lives. I noticed a definite bond between all the girls in my colonies. The mice definitely become familiar with each other, and having strange females grouped together is another point of stress.

Hope this helps.