I don't know what's wrong with your chick for sure, but I can tell you that a water leak can indeed cause a horribly severe ammonia problem, if the leak is bad enough. While we were out of town and our usual chicken sitter was at camp, my daughter-in-law took over Katie's duties. On the day were were on our way home, she started the lawn watering tractor (that little tractor that puts along the "track" of the garden hose to water lawns) and then went back home. She totally forgot about it. We usually put the little stopper on it before the spray reached the chicken run, but she didn't. The tractor hit the side of the run, jumped the track, and pumped water into the run all day long. We got home about 6 hours later and rushed to turn off that hose. Food containers were swimming in water. The dust bath bin was a lake and it was running over. The chickens had retreated to the coop. Our deep litter was quite literally floating. After we cleaned up the mess, we removed as much saturated litter as we could, and turned over what was left to begin the drying process. It was really windy that l night and we kept turning that litter, adding more dry to it, whatever we could think of. Jenny felt horrible but it was just an accident.
The next morning I woke up to the smell of ammonia - in my bedroom. I ran out in my jammies and the smell before I even got as far as the coop about knocked me over. My eyes were burning and watering, and I could barely breathe. It took over a week to get that run dried out and get the new deep litter to where it could start working again. DL needs a little moisture to work, not the Great Flood! We still had a slight ammonia smell for almost two weeks, until things got totally dry. The chickens were relegated to their coop and free time in the yard, but denied access to the run. I have never smelled anything that strong and repulsive. Even my neighbors were asking me why my setup started stinking when it never had before. A couple of my chickens ended up with swollen eyes and were kind of lethargic and off their feed for the first few days, but they recovered. I didn't do anything for them - I didn't know if anything but fresh air, clean food, and plenty of fresh water would help anyway.
All that said, I still wouldn't be quite so quick to accept the "ammonia poisoning" explanation either, even though I know first hand it's possible. I think I'd be more worried about the potential of bringing some kind of pathogen or infection into my set-up. I'm just pointing out that ammonia can really be that serious.
