I may be way off base here, but it sounds like you might be putting too much pressure on your legs and not focusing enough on having your core do the work.
I had been having a similar problem only with my legs in PLB where my calves were hurting on one of the exercises for the glutes (the one where you are on your back with your glutes up and rolling the ball in towards your glutes). I realized I was too focused on trying to keep a hold of the stability ball and putting all kinds of pressure on my feet and calves. Once I relaxed and focused on my glutes my calves quit trying to do all the work!
Just a suggestion!