I've been cloth diapering for over seven years, and I bet the problem is your detergent. The F&C are the worst of the worst. You need to also look up the hardness of your water, as minerals In the water can react with your detergent and leave a stinky residue.
Dreft is terrible for cloth diapers too.
As far as grocery brands, I had good luck with regular Tide and Planet. But I switched to Rockin Green and all the problems went away.
Meanwhile, wash those covers with regular blue Dawn (google stripping cloth diapers) and start over, basically.