This is well known and we've been able to recreate the mechanism built in the original stop mo models (search for vids into the studio scale section).
The pistons are not intented to move independantly, when it happens in the movie that's because the mechanism was broken and they did not want to reshot the whole sequence. They animated the pistons by hand in this case.
The original mechanism allows the pistons to move without having to animate them by hand. When you animate the leg one piston moves up and the other move down. Unfortunatly this is a very delicate and fragile mechanism.