Well I called them today and they just could not seem to locate my foot control or cord. They don't understand how this could have happened. Since Janome no longer makes this kind of foot control there really isn't anything they can do.
Well I did some checking and Amazon has the foot control for $70. Not sure I can force them to buy it for me so maybe the only thing I can do is report them to the BBB.
I telling someone at my LQS about this, she said she has heard of some places keeping "nicer, newer" parts and giving people back older, crappier parts. I still don't know if this is deliberate or not but I know I will never go back there again... AND I will always mark my parts.