Agreed. I spent about 4 hours last Tuesday working on Manta's flipper. It actually uses a piston to push the flipper up. This is really rough on the game physics engine. In Manta's case the piston is really close to the hinge, which makes the piston prone to penetrating so far that the physics engine breaks.
I suspect we have pushed this approach past its limits, and we are going to need to take a different approach for flippers in the future. This is the biggest reason that we haven't included pneumatics in the Robot Workshop. We need to make sure the system is stable enough to handle any geometry.