Sorry for the late reply, but I've looked up many pictures of skin chafing, and I don't think that's what I'm experiencing. When I said running in jeans, I don't actually mean a long run, but maybe just running to get the door when it rings, or something like that. And some of the areas that have this problem are covered by my boxer.
To add a bit more details, it usually starts out as a red dot, kind of like a pimple, then it would get bigger (i think depending on how much running I did or how much contact it gets). It is elevated at first, then it'll smooth out, but leave a dark patch (like a scar?) then it'll fade over time.
There is absolutely no abscess or discharge of any type. I don't think it's any type of fungal infection.
Of all the pictures I've seen so far... I think what I have is some form of rash. But I don't quite know the cause behind it... Is it possible to get a rash from wearing boxers in general?
As stated above, do not run in jeans. There is a reason people running track or jogging down the street do not wear jeans while doing so. You have some skin chafing going on. Its common in both thighs and buttocks. Running in any material not suitable for running in will cause this, as well as a possible sensativity to a certain material or detergent, wearing too tight of pants / underwear, or being overweight. There are other causes, but one or more of the above mentioned is likely your issue. Its no biggie, my husband has always had it on his rear and I have seen several others with this issue. Try correcting any issues with anything I have suggested, and if it doesnt go away, its purely cosmetic and you will be fine.
Do not run in jeans. I don't know why you would anyway. Do you neverhave problems with jeans, unless you run?