I got awful ammonia when we moved to Hawaii. I had to use oxiclean + vinegar to break up the ammonia salts to fully get the diapers clean. It was like a hard reset so I could work with my new wash routine. I used my camp washer that I had for the hand washing flats challenge to soak and agitate the diapers in the oxiclean vinegar and super got water for several hours, then washed normally and the funk was gone.
Is your detergent you are using on your clothes working well in your water? I've found my water here to be awful so when tide worked on my husbands boat clothes it became my only detergent and works like a charm. If you have something working for your clothes try that for your diapers to see how it works.
Don't give up, laundry issues can be handled!
Married to my best friend, living the navy wife life, and loving every minute of being a SAHM to DS (born July 2011)!