I have put bodyglide on down under when I am going to be in tri shorts for a decent run especially after swimming/riding. I noticed when I didn't that I had marks there, even if I wasn't conscious of them while running.

Have you tried bodyglide or aquaphor or anything? Not something you could do in transition, but it might last you through the swim/bike since they are less chafe-y in that department (well, maybe the bike).