I'm replying to a post or two back, but I thought I'd just keep the flow going 
It really sounds like your turtle or turtles have eye infections. These could be connected to upper respiratory infections, but you would normally see other symptoms like noisey breathing or nasal discharge. Eye infections can be brought about by several different things.
-lack of adequate Vit. A in the diet
-enclosure too dry or too wet
-consistently too low or even too high temperatures
-dirty water
-irritant in the enclosure
-there have been cases of virulent fungi being carried by dried sphagnum moss from Asia
-etc.
Infections can be viral, bacterial, or even fungal. Only a qualified herp vet should be looked to for diagnosis. Then, only a qualified herp vet can give you the proper medication...or maybe none at all. Your issue is going to be obtaining a medication that can be dosed for such a small turtle. It can be done.
In the meantime, it's always a good idea to completely re-evaluate your husbandry. I'm not saying that you are or are not doing the things that you need to. I'm not saying that you caused the problem. However, it must always be considered. Read all you can about rearing hatchling box turtles.
Please allow me to add a few recommendations. It sounds like you're handling your hatchlings a lot. I could be wrong, but it just sounds like it. Hatchlings are notoriously skittish and prefer to hide nearly all of the time. Handling should be kept to an absolute minimum. This includes handling for feeding and soaking. You will notice a marked difference as time goes by, and your turtle may actually begin to enjoy a small amount of handling...based of course on the fact that they're being fed or enjoying a good drink. It typically takes months to years. If the turtles are stressed, it might lower their immune sytems and leave them vulnerable to infections and illnesses.
Also, I'd refrain from the Pedialyte baths. Pedialyte is kind of a "last resort" type of treatment. It is normally used in cases where herps are anorexic, and Pedialyte is really one of the only ways to get essential electrolytes and some other nutrients into them. One year, I went out and purchased several bottles of Pedialyte and soaked my outdoor box turtles for several hours. It was just about this time of year, and the turtles were beginning to show signs of hibernation. I figured that I'd give them a nice hydration session before they bedded down. Well, half of them woke up in the spring with eye infections. I was able to treat them with an antibiotic eye drop. I think it also contained a mild steroid. I don't know if the Pedialyte had anything to do with it, since it was a very wet and mild winter. It's just too coincidental. If the turtles are still eating well, I'd just stick with plain old water.
Last year, I built a custom-made wall mounted shelf for raising young turtles. It was constructed to conserve heat and electricity. Well, the bottom shelf was not getting warm enough. The turtles were being maintained at only 70 degrees F or thereabouts. There were Three-toes and Ornates on that particular shelf. In only the week or two it took before I could find time to address the issue, several of each species started acting much like yours...swollen eyes and lethargy. After another two weeks or so of warmth, plenty of vitamins, and daily soaks in warm water they were fine. However, mine never had any type of discharge. If they did, it would have been off to the Vet.
I'm sorry about the long post, but I am concerned about your hatchlings. It is a VERY good thing that they are still eating. By the way, the hatchling above (in your picture) is probably the most stunning Three-toed hatchling I've ever seen. The other one is pretty also. Good Luck! Please keep us posted.