It may be gill flukes, based on the fact that she has been breathing heavily for a week. It could also just be that she was stressed. Were the water parameters in the two tanks quite different? What about the temperature? When in doubt, add some aquarium salt. A little bit shouldn't bother the other fry in the tank. How often are your water changes? Could it be that there is too much CO2/ not enough O2 in the water? If so, try adding an airstone and doing more frequent water changes. Sorry I can't be of more help, I've never had to deal with gill flukes before.
Last week I noticed one of my 5 month old female guppy breathing heavy. She's in a 2.5 gallon tank with a bio wheel filter. The other fry in the tank are breathing normally and shows no signs of gasping for air. A few days ago, I tried to move her into my 29 gallon tank which just finished cycling. As soon as I moved her into a bag, I immediatly noticed that she was breathing very heavy so I put her back in the fry tank. 
Her heavy breathing continued. She goes up to the surface to eat, but for the rest of the time she stays at the botton and often sits on the gravel gasping. Could it be gill flukes? I really need some urgent advice! 
Before I attempted to move her into the larger tank, I tested both of the water chemisty and everything looked the same. The temperature in the fry tank is steady and it has a small heater designed for small aquariums. I do 25 - 30% water changes once every week and the filter is wroking normally. Sadly the guppy that was gasping died. 
Unfortunately, fry are very delicate and it is hard to cure them once they have developed a disease. Many people recommend doing daily water changes in their fry tanks because fry are so sensitive to poor water conditions. I hope someone else comes along who can help you better than I can.
I'll try to do water changes twice a week. I decided to move the female guppy that was breathing hard into my 29 gallon tank that just finsihed cycling. I tested the water carefully and all looked stable and safe. After I released her into the tank, she was still breathing heavy so I dropped in an air pump just in case there wasn't enough oxygen even though the tank has an Aquaclear filter. 
I'm concerned about her because she's laying on the gravel and still gasping for air. I don't want her to die! What's wrong! 
