We had something similar with DS. Was only his penis tip and down the side. Initially he was Dx with herpes. They said it was from someone changing him with a cold sore and that he'd have it forever. I was horrified. DH and I don't get them and the only person who would have changed him (and only once or twice) would have been my mum. He was put on zovirax and it seemed to go away, but it co-incided with him being put into disposables. We moved to Darwin for 3 months and used disposables while we were there as there was no room in our luggage for cloth. No issue while we were there.
Then when we moved into our house and started using cloth again it came back. I took him to a new GP and she swabbed him. Nothing grew and he came back negative for herpes. I stripped my nappies and rinsed heaps adding dettol and tea tree to the wash. Never ever came back again.