I'm sorry. I can imagine a little of how incredibly frustrating this is. With conscientious care like you are giving, it seems like no good deed should go unpunished.

Have you been feeding your guppies brine shrimp? Have you gone to the trouble of hatching baby brine? Might there be left overs in the tank?

(I hope that right here your answers to the above are all no. However I have done that and seen the following with other species.)

Take a flashlight and shine it on the fry. Also take a look at the adults. Look closely to see if there are little tiny almost microscopic dots. These may appear as a rusty, gold or whitish sheen.

If that is there, your fish very possibly have velvet or Oodinium. It is not common among guppies, but it is known to attack them once in a while.

I wonder if spores of that disease actually float in the air. Or maybe the organisms are almost always on the fish in small numbers - and limited by a fish's immune system.

Over feeding brine shrimp seems to set up an environment where their population just explodes or "blooms". They can cover a fish's epidermous - both their skin and their gills. The pattern of losing first tiny fry, then small fry, larger fry, less dominant adults and dominant adults is often the way it attacks fish tanks.

It is very easily carried from one tank to another on your hands, with equipment or with that Murphy's law splash. You mentioned that you had five tanks and have some of those fish in a hospital tank - a great idea by the way. But also watch that tank and scan the fish with a flashligh beam.

Scrub down your hands. At the least dry out your siphon hose and bucket outside in the sun and weather. If it is freezing, so much the better. You may want to soak them in a 1 part bleach, 10 parts water solution.

If this seems to be what is attacking your fish, you may want to do 20-45% a partial water change. Gravel grunge the tank bottom especially. Add water as warm as what is there. Add 1 teaspoon of salt for every real gallon of water in the tank. Turn off the tank lights. You may even want to masking tape newspaper or sides of a paper grocery bag on the tank sides to cut down light.

Velvet organisms are protists which both parasitize fish and live by photosynthesis. The lack of light and medications interrupt the photosynthesis and hopefully give the fish's immune system a chance to fight back.

Many of the medicines sold to combat velvet (usually on Bettas, anabandids, rainbowfish, some pleco types and killifish) have a medicinal dye called acriflavin in it. One brand name of acriflavin is called Bamiflavin. The green of the dye may very well also interrupt the photosynthetic cycle of the velvet.

Aquatronics makes an Acriflavin Plus (acriflavin plus an antibiotic to help with secondary infections). Jungle markets velvet guard. Mardel has something - sorry I don't know which item - which seems to have been effective for aquarists. There are other offerings by the manufacturers

I would administer the medicine you select - IF this is velvet - according to the manufacturer's instructions. Three days later I would make another 40% water change and maybe add salt at half the original rate. Also re-administer the medicine - if that agrees with the manufacturer's instructions.

Continue to monitor your fish with that flashlight. Don't get infected water on it please. ;)

You may have to continue a regime of those water changes for a while more.

If you don't see tiny dots or a dusty sheen to your guppies, I'm sorry to have wasted your time.

And while I hope this isn't velvet you are up against, I hope this is of use if it is. :)

Let us know what it was.

Good luck and all the best!

unclescott