That is a pretty impressive filter system, water quality. I have got to ask though, are you sure that the power filter isn't just sucking the fry up? If that was happening, the size of the broods would be explained.

You don't mention tank mates or what you are feeding the females before they drop. Those factors can also limit or encourage cannibalism. For a lot more on this, please see Immediate Help, especially the sections on
# Breeding
# Pregnancy and Birth
# Sexing Fry
# Fry Diet and Safety

The limited brood size and fragility of the females could also be attributable to a variety of internal parasites. Most of us (me too in the past) don't think to quarantine new purchases and during that 2-4 week period, treat them with an anti-parasite combo. Treating for internal parasites is best, maybe three days before they are taken out of quarantine and gradually acclimated to the regular aquarium. That way they don't stay with the treatment chemicals or any dead parasites.

I also wonder how long your aquarium has been set up. Has it cycled? Do you have test kits and do the ammonia and nitrite readings read at about zero. Are the less toxic nitrates still at safe levels. If this stuff seems old hat to you, I apologize for wasting your time. If you aren't sure what these questions are all about, please again check out Immediate Help and
New Tank/Cycling/Setting Up/Water Changing

Also in that section is a little ditty on
Acclimating New Fish to a New Aquarium.
Are you gradually acclimating the new females to their new home and then tossing out all of the pet shop water? Some fish can be rushed into a new tank if their water chemistries are much the same. In other cases, abrupt changes will mess up some of the gills, even bursting some of them and the fish will die later of suffocation or some disease which they are too weak to resist, especially after a stressful situation.

Are there things in the air which might effect the females? Bug sprays, pest strips, painting or paint stripping chemicals and the like can have a powerfully devastating effect on a fish tank. Likewise, this time of the year one wants to make sure that not only is a tank's heater keeping the guppies at 76-78 degrees F/ 24.4-25.5C important, but so is keeping the tank out of drafts and hot air blasts from vents.

By the bye, in time (within a month would be good - Dear Santa...) remove the fry to a larger aquarium or they will stunt. The more room one (clean water, great food without overfeedin, approrpriate temperature....) can give a fish, the faster and stronger they will grow.

New Guppy Momma has some asked some really important questions and given some great advice. Please consider her comments foremost and mine as merely supplementary.

I knew a very experienced aquarist who has a municipal water supply, which seemed fine for raising his young fish in. But no matter what he did with new fish, they died within a short time of purchase. He kept mostly egg layers and had a one month rule. He made himself set up new acquisitions in spawning set-ups within the first month he had the fish. If he were keeping guppies, you know that he would work to save the first and second batches of fry from a pair.

Eggs were usually laid and hatched. The fry almost always grew up strong and beautiful. So he did what he had to do to succeed in the hobby.

I wonder how many of us would "stay in fish" if we had to deal with the challenges he had. Even after quarantining new fish, maybe giving them a preventative anti-parasite treatment, carefully acclimating them to his tanks and never introducing any of their carrying water (obviously except for what was on the fish's bodies), feeding them the best foods, doing significant partial weekly water changes with treated, seasoned water. he lost an astonishing number of new fish. He persevered to build a wonderful fishroom, win fish shows, mail Bettas and killies around the country, join and even help start fish clubs, create media presentations on his fish and speak at clubs from time to time during the decades he was in the hobby.