Same thing happened to me. I'm chicken-sitting for neighbor's 6 hens until May. She has a tiny coop with a pop door that is open 24/7, as well as circular vents on north and south sides. About four days ago when I opened the top flap to stir shavings and collect eggs, the ammonia just about knocked me out. This, even when I stir twice a day and add shavings when I deem necessary. Today, since it's the weekend I chose to remove all the shavings and add new. I could tell it wasn't going to get better! Even with all the airflow and constant stirring, my opinion is that her coop is just so small it's going to be necessary to do this at times. An added annoyance is the water container that is sitting on the heating thingy, is not very far above the shavings so when I change the water I constantly get overflow in the coop because the coop isn't large enough to remove the two gallon waterer. I have to take the top off, lift the base, rinse it, place it back on the heater pan, then fill, then replace the cover. When I replace it, no matter how slowly I push it back down, the water squirts from the trough into the coop. Then I have to remove wet shavings.
On the upside, I know now that I won't be getting the same type of waterer for my flock. She's limited because of the size of the coop. I wish I could hang it, but no dice.
At least I have lots of compost cooking right now!