I've heard of this issue with the 3m clear bra applications. I was going to take my car to a shop to have that done and they said they would only apply it to the original factory paint. They would not apply it to a non-factory paint job (mine is the original so it was a non-issue). So, sounds like this could be a common problem with vinyl on re-painted surfaces.
Sorry. Don't you love Monday morning quarterbacks?