This happened to us about a month back... :( Not fun. It was longer between washes because I had to go to my mother's to do it and we're still working on trying to clear up a rash which I assume was caused by the diapers sitting too long in between. She had never had a rash like that before. Only slight redness.
We went from a top loader to a front loader as well... and it does seem harder to get them clean...and I notice the smell of DH's scented detergent (I wash mine and hers in scent free) lingering on the diapers from the wash... so I'm hoping we dont get build up issues from that. I've tried extra rinses and the towel trick, but without much luck.
I ordered some grapefruit seed extract to add to the laundry to see if I can disinfect them.
sigh.
no advice, sorry.