i would bleach them periodically, and yes - stink means they're not getting clean. wash with plenty of detergent (i use country save - cloth diaper safe, cheap, doesn't irritate my girl's sensitive skin), skip the potentially irritating essential oils. instead of repeated rinsing, run them through an extra hot cycle with no detergent.
i'll also second the move to natural fibres (we use organic cotton prefolds and wraps) if possible to see if that makes a difference. my girl's skin got rashy with synthetic fibres in pockets. i had to strip them frequently - i think they're just prone to that.