Did the vet do a scraping on either of your dogs? They'd be able to see mites if any were present.
Could your dogs just have dry skin? Our dogs always get itchy in fall through the winter unless we supplement with omega-3 oils. Right now they're on salmon oil and it cleared the problem up pretty quickly--we noticed less itching after just a couple of weeks.
I hope you can get a handle on the scabies. Sounds miserable!