Good news, there is a quick fix!
Yep, plain old white vinegar!
You can do this a couple of ways.
Pre-rinse & add 2 cups of vinegar
Wash as usual, but to final rinse add 1/2 cup of vinegar – or put it in a downy ball.
or (this is what I do)
Cold wash as usual
Warm wash – NO detergent – add 2 cups of vinegar
Hot wash as usual, but to final rinse add 1/2 cup of vinegar – or put it in a downy ball.
Dry as you choose 
If the problem persists, try adding a bit of vinegar to the wash every time you do your diaper laundry. You might also try using a bit less detergent in your normal wash routine, as buildup and make it worse.
Another tip that I’ve seen and am currently using with great results is an open pail. I keep our pail in the bathroom closet and just don’t put the lid on. It seems to be working great!
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This site has washing instructions, including a suggestion for using baking soda & vinegar for stinky diapers (select #7 – washing instructions in the drop-down box, & scroll to the bottom):
http://www.jilliansdrawers.com/newtocloth
Option #2 has been working great for us! Thank you so much.
I keep an open pail in the laundry room for CDs. No ammonia issues yet. I wash every other day.
Thanks for the vinegar tip in case I need it!