Sounds like a yeast infection from the moisture in the pull-up. My daughter is now potty trained at night, but last summer or the summer before, she developed a series of yeast infections without being on antibiotics. I figured it was due to her full nighttime diapers, low circulation of air getting inside the diaper/pullup and the increased temperatures from warm summer nights.
My advice is to apply some 7-day yeast infection cream to his bottom morning and night for the next 5 days and see if that clears it up... And if it does, keep sone handy in case it pops up again--summer has only just started!