The first thing is to be sure your BF's penile rash in fact is due to a fungus (yeast). The apparent response to an antifungal cream may be coincidental. Penile yeast infections rarely come and go with the frequency your question implies; and a penile yeast infection would not show up immediately after sex, it would take several days.
That said, many women carry yeasts in their vaginas, without symptoms. I can't be sure that isn't the problem. I suggest you and your partner go together to a health care provider with expertise in STDs and genital infections. You might start with your local health department STD clinic, or a gynecologist with particular expertise in genital infections. Most academic medical centers have such experts.
Good luck-- HHH, MD