I had/have a similar problem with my older son (he's almost two and still in diapers, but we've had to switch him to disposables for other reasons). I tried baking soda in the wash, vinegar in the rinse, borax, bleach on my prefolds, air and dryer drying, anything I could think of. Nothing really worked for me, but I think air-drying outside in the sun was the best. I use a dry-bucket method of washing, and that could also contribute to smells being trapped in the diapers, though I don't have the problem with my infant's diapers smelling unless my toddler is wearing one and poops in it- then the entire wash load smells bad. Maybe it has something to do with their poop after they start solid foods? You didn't mention how old your son was or if he's started solids yet. You might try washing poopy diapers separately, and see if that helps, also.
Something I recently learned about the Fuzzi Bunz diapers (I have a few, but not a lot) is that the PUL fabric the outside is made of was first designed to be used in hospitals as a waterproof barrier, and meant to be autoclaved (sterilized at a high heat). It can withstand anything a normal washer and dryer can do to it, and keeps its seal better if it has the higher heat. I think the manufacturers of Fuzzi Bunz recommend natural detergent, etc. more for the baby's skin and/or environmental reasons than because it's necessary for the diapers.
I hope this helps. Sorry if it's confusing or more than you wanted to know.