I've seen that a lot. We have a product in the marine industry called Corroseal. Ships get rusty due to the salt water so they put Corroseal on the rust which stops it from spreading. Plus you can paint over it. There has to be a product in the automotive aftermarket like this. If not try to find Corroseal, it's $50 a gallon.
I second the POR 15. Good stuff. Also check into rust encapsulator at www.eastwood.com. It comes in an aerosol unlike POR 15.