Moisture is kinda the same as rust.. Once it starts in deep into the material, it'll keep going.. That's why they call it "cancer" when it gets to that point.
Surface rust or moisture that's just gotten to the surface can be stopped if you catch it in time (same deal with real "cancer" too)
Anyway, it sounds like you are going to have to do some serious surgery and cut out the rotted wood and replace.
That should stop the spread for the most part. It might stop on it's own, but you will still have the soft spots, so might as well fix that up anyway?
Good luck!
Mitch
