As I don't have PLE, I am unable to take a look at your file. However, it sounds like you are attempting to make 2 different nodes control the joints, those nodes being the joints (animation set, Skeleton > joints) and the object constraints. These two things together won't work well. When you skin to joints, all the skinned objects transforms get blocked out, so that m/any constraints will become useless. You are going to have to figure out how you want to set up your legs and stick with it.

Also, the reason your geometry keeps deforming with rigid bind is, despite being rigid, it is not devoid of deformations. Some of the geometry will still bend and shift to maintain it's connection with the joint. What you will want to do (and this will also help maintain some of the constraints created earlier) is to group all things attached to one area of the leg (all Thigh items, for example), and then parent constrain that group to the appropriate joint.

Hope you'll be able to make use of some of this. Good luck.