the only way to fix rust is to completly remove it and weld in new metal. its like a cancer for cars, once its in you can paint no end of rust resistant primer, rust killer/bodyfiller and grind as much rust off as you like it will always come back. it was the only thing putting me off getting a datsun 240z or a ra22 celica gt (classic jap motors from the late 60's/70s) after doing 2 full major restorations on my last 2 crx's (i have had over 6 of those) you get used to dealing with it.
if you are going to insist on using a rust killer do as above and grind as much out as you can, rust killer the metal thats left then paint a 2 part high solid content epoxy base/primer over it. epoxymastic is fantastic (and silly expensiave) but its sooo dammed good, it seals the metal or what ever you paint completly from oxygen and moisture (makes hammerite look like watercolor paint) its also suitable for wetsanding down and its 2 pac paint safe
