I'm seeing the same price differences as well, I'm just going by a multi-city search I did on the website, which you should do yourself, so you can see the numbers in-front of you. There was no additional charge that resembled a "stopover charge." I can't find any reference to a charge for stopovers in the list of fees, or in the two rules that describe stopovers. If there were indeed a charge, I'd hope it was listed and not "hidden" somewhere. Seems frustrating, so I hope you can find a fare you're comfortable with!