Toby's had nappy rash on and off since he was 2 weeks old (he's almost 5 weeks now). We've been to the GP a few times and it's not bacterial or fungal. The only thing that has cleared it up has been 1% cortisone cream but I can't (and don't want to) use it all the time.
So here's what we've tried (obviously not all at once):
Changing laundry detergent for cloth nappies
Not using baby wipes (just water and a cloth)
He had lots of nappy free time, I always dry his bottom after changing him. Desitin and corn flour are the best barriers we've found so far but they still don't fix it.
the GP took a swab from it and it was all clear.