Seborrheic keratoses are raised, brown "age spots," which people get on the face and torso, mostly in middle-age or older. When younger people get them in the groin, they are usually warts rather than keratoses, though the pathology may not show viral particles.
If your wife doesn't have them, all she needs to do is have regular Pap smears, which she likely does anyway. Often, partners of people with warts never get visible ones. As to where you got them, the question is basically unanswerable (just as it would be on the hands or feet), and it really doesn't matter.
As for treatment, all warts recur when they want to. You just need to keep after them by some noninvasive method. Sooner or later, the "give up," and stop recurring.
Freezinf them in my experience does not usually scar--I suspect you just have some residual pigment, which will go away in time.
I advise you to consult with a dermatologiwst about available options--freezing, burning, self-application of a cream such as Condylox or Aldara, and so forth.
Chafing is not a factor.