Good call Kelly, chances are that the issue you have related to the lead joint between the roof and the rear quarter...It's best to remove the damaged area 1 layer at a time to see not only how the problem occurred but, to also find a remedy. As you remove the top coats check for discoloration between layers, check for any signs of moisture between layers. If there is moisture between layers that means that the moisture was trapped when painting. It could have happened in the priming process which may indicate that the lead seam is fine, or this could happen if the lead filled seam was disturbed during the initial prep during the first paint job. look to see if there is regular filler over top of the lead and try to remove some of the plastic filler by prying it off. Look at the underside of the filler for again, discoloration. Then as mentioned, if there is discoloration remove the lead, clean the area (use a sandblaster to remove any rust and with a 50 grit disc, grind the area, apply a coat of Epoxy primer, and fill the area with a plastic filler. Block sand to make the C Pillar straight, apply at least 2 more coats of a sandable epoxy primer. Allow the Epoxy primer to cure, final block, for base coat I would recommend 400 grit dry or 600 grit wet (800 grit wet if your using water born base), base the area and clear.
And to add to Kelly's comment about using primers other than epoxy over a lead filled seam, your right Kelly, before plastic fillers, all panels where either replaced, repaired by a pick and file method and lacquer primed, or filled with lead and primed with a lacquer primer. During those times, lacquer primer was brushed on, sanded and then painted with lacquer paint. Materials have evolved over time and Epoxy Primmer is a big step forward in substrates compared to lacquer or even etch primer.
Taking the top coats off one layer at a time will tell you the story of what happened and give you the information you may need to avoid a problem like this in the future.
I hope this helps.