Oh Man, If I were you I'd tell him to his face.

I had a similar situation years ago with my first job.
First, I asked him if he had a medical problem.
When I got the puzzled look I told him to get some stronger soap because his didn't work.
And I asked him if he realized that he grabbed his crotch every few minutes. I told him maybe he had a medical skin issue because of the smell and apparent itchiness.

He never came into my office again unless he absolutely had to.