My guess is that it's the shape of the saddle. In the past year I've ridden nearly 4,000 miles in jeans and khakis without having this problem. I dumped the wide, "comfort" saddle that came with my bike in favor of a narrower one. Considerably less rubbing on the thighs.
Not sure how that fits with the theft problem you describe. Perhaps a locking seatpost clamp (like Pitlocks) or the more traditional method of looping a length of bicycle chain between the seat rails and a seatstay.