DS had this same problem. It ended up being the wipes and I don't use them anymore. I just use flannels with water.
Also Moogoo is AMAZING for nappy rash. We used it to clear up a nasty bout and now after every bath we put a bit on the area's he's prone to (the area's you mentioed and also in the little fat rolls) and he hasn't had nappyrash since.