Hot water not only can set stains, but it can lock in the smell too. Try a cold pre-wash, a hot wash, then a cold rinse to clean your diapers thoroughly. If this is your problem, run your diapers through several wash cycles, without adding anything to the water. Keep washing till the water runs clear - no bubbles. As a result the diapers are not being properly cleaned, through all the layers.
Polyester is famous for holding in smells.
Check to see if your diapers or covers have polyester in them. Even a small amount can be a problem. Mother-ease diapers and covers and Bummis Super Industrial Wraps are often the stinky diapers and covers in question. Vinegar is acidic as well, so it will only exacerbate the problem. Dr. Bonners , or other vegetable-based soaps don't seem to be working for some with very hard water.