Just called Zinsser. Not surprisingly, they said it's probably the topcoat. They also suggested that it (the top coat) might just require more time to cure. I doubt that though. 1.5 months, and the odor/softness doesn't seem to be getting any better.
What a pain. All I want to know is the easiest way to repair it. Can't wait to figure that out. I'm going to go back to the Sherwin Williams store today and see what they recommend for repair, although they'll probably say scrape/sand and repaint.