I have the same issue with pod hd pro. I have tried several pedals including the mission pedal on the hd pro and it will not start when you turn on the pod.
I also have a hd 500 and the issue is not present here, i have used mission ep1-l6, Roland FV-500H and Ernie ball vp-junior all with great success. Today i tried the bean version and it also was a success. This leads me to think that it is a fault in the programming on the Pod Hd Pro. I have also the fbv custom footcontroll (the one that belongs to vetta) with 2 exp pedals on it and this works like it supposed to do both the pedals are working when you have turned it on.