I've looked at a lot of Gen 5s with the same problem. When they are repainted, the paint doesn't stick to the caulking between the bed walls and the bed floor. I don't know if it is from stripper getting into it or if it just hard to make paint stick to. Does anyone have a clue as to how to keep it from peeling a year after painting?

I know exactly the problem you're talking about.When I repainted mine a few years back, all the old sealant was removed and I used a product called"Drip rail and body check sealant". Believe it was from 3M and it came in a caulking tube, a very thick black mastic type compound. You apply the sealant like caulking then spread it either with a wooden popsicle stick or a wet finger. It's paintable, the paint doesn't peel off but you still get some small cracks after a while.
El Camino bed (http://elcaminocentral.com/gallery-photo_oldelky80-SS396-El_Camino_003.html)