I would normally say RTFM, but sounds like you are one of the rare birds that already does this sort of thing - so, I guess it is "complain to the vendor(s)" - while two people may indeed agree on how to represent a spot color in a PDF, in JDF - it the Schema is often not a clear, so two vendors might be using different tags or approaches. I had a heck of a time getting 5 vendors consume and properly process something much simpler ( a tray pull ) via JDF years ago, so, while you might "hope" that JDF is a 'standard' - it is really up for interpretation ( yes, pun intended )
Michael Jahn - Slightly used PDF Evangelist
Simi Valley California