First, absolutely positively raise the waterer up as high as the chickens' backs. Also make sure it is located out of the way, not in a high-traffic area or where they jump down from the roost.
Second, what kind of ventilation do you have? Is there anything other than the two windows? Which I'm guessing you do not leave open at night or on cold windy days? If there's no other vents, make some, high up under the eaves, and leave them permanently open. Good sized vents, mind, not just round holes 
Third, is that mesh shelf sort of a droppings-pit arrangment under a roost? Replace it with a solid shelf, and scrape the poo off every morning (it takes about 5 seconds; use a dustpan to push stuff off the edge into a bucket for disposal). That will keep the litter much less pooey and drier.
Finally, w/r/t the waterers: CHECK them for leakage. Whichever one you're not using at the moment, clean it and fill it and put it on a level surface in the garage or some such thing, on concrete or any other surface that will easily show leakage. If it really is leaking, get new waterers. Alternatively is it possible your coop is not dead level (or that the waterers are sitting unlevelly on the bedding)? If the waterer isn't level then yes the water will siphon out and make a wet mess. To some extent you can avoid this by turning the waterer so the hole where water comes out is ont he low side -- but the BASIC fix is just to ensure it's on a level base 
Good luck, have fun,
Pat