Jonathan, this could have been caused by a number of different reasons. Yes, polyester body filler is going to expand and contract at different rates than the metal it is on. But if used correctly, it will out last you and I, the truck will be rusting away in the wrecking yard and it will still be there!

What you did was the just the wrong way to do it, and you knew it when you did it.

You were planing on a temporary repair and you got it

Believe me, I know, I have did similar things.
The object is to use as little as possible, this is true. I like to "metal finish" (repair the metal so no filler is used at all) whenever possible. But many times that is just not practical or even possible.
Next time you try to push the envelope of filler use

try one of the water proof fiberglass or metal reinforced fillers. Evercoats "Kitty hair" or "Tiger hair" (you can fill holes 3" wide or more with Tiger hair) or "Metal to Metal." I have to say again, it is NOT the proper way to repair these holes (but you know that) but I have seen Kitty and Tiger Hair used to "repair" some pretty badly rusted things work dang good. Before I was repping paint, I would have never said this, but I have to say, I have seen it do some amazing things that lasted years.
Good luck.