I'm not sure about a fungus, but I know a little about a yeast infection. Is that what you mean? When I suspected a yeast infection that didn't go away even with antifungal cream, I boiled the diapers and cloth wipes in a big pot on the stove. It was a pain in the butt, but all for the sake of a darling little butt! Ha ha. My daughted ended up not having yeast, but my diapers have never been so clean! By the way, I boiled them when they were clean out of the machine- it seems obvious but when I told my sister I was boiling them she got totally grossed out. I also used vinegar in the rinse thereafter, and sprayed them with tea tree oil. There are some previous posts on there about yeast infection.
Another thing...I just reread your post. You don't want the rash to spread to your other babies, so try to keep the boiled diapers exclusively for the boy with a rash. You'll need two diaper pails. I had to do this for a bit because my baby and toddler both wear the OS diapers. Good luck!