My Flying Fox doesn't have the "teeth" to hurt plants. Although "Flying Fox" is probably a collection of different species, so there is a possibility that some do, some don't. I have seen Bristlenose Plecos doing some serious damage to swords, but if you don't have any...
Could be lack of certain nutrients. Potassium deficiencies can cause holes in leaves, but they are usually not starting out transparent.
its a 50 gallon with 126 watts of fluorescent lighting. I dose with seachmen products, I dose usually bi weekly with nitrogen, K, trace, phoshporus, Fe, and flourish and then do a 50 % wc weekly. I have pressurized co2 that runs at about 3-4 bps.
Okay.... I don't think the Flying Fox is the problem. I would have guessed nutrients, specifically K, but since you dose everything, that shouldn't be the problem either. BTW Seachem K is not very concentrated, finding some K2SO4 might be more cost efficient. That's besides the topic of course.
If the plants have been put into the tank fairly recently, it is possible that they came from a different environment, and dying leaves is just part of their adjustment.
Another nutrient-related issue could be a lack of nutrients in the substrate. Swords are root feeders, and if your substrate is inert gravel they will definitely suffer. If that is the case, I would suggest some root tabs or even a few Jobes sticks here and there, that should green them up a bit.