jdmfreak,
I had a '99 that I brought to the dealer and I believe it was a 5 year 100,000mile warranty but I may be wrong... anyways I had them check the bubbling on my door (drivers side only) and they ended up replacing the whole door.
The one catch I was told by the autobody guy (contracted out) was that they don't do "color matching". Basically they won't pay to match for fade. In my truck it was no problem because it was black but he told me red trucks can be pretty noticable, so please keep that in mind.
Other than that why would you hesitate to have them repair it for free? Down the road you will regret it whether you keep it or were trying to sell it. . because it's only going to get worse and get worse real fast... .