What you are experiencing is called "double transforms", it all has to do with your hierarchy and the order of things.
Typically when I rig I have it all organized in different groups, one group being geometry, the other is joints, another are the controllers which I see you don't have any and the other ones can be miscellaneous.
First of all I notice you have nurbs, the industry today is more towards polygon meshes rather than curbs to start off with.
Secondly, you never want animators to animate from the joints and never freeze transforms joints, its just something you don't do, you freeze transforms controllers once you place them on the joint's pivot point. Reason we freeze transforms those controls is because if animators wish to bring the controller back to its original position it needs to have a new default pose which is why we freeze transforms. The way you can easily go about making a connection with the controller and joint is with a constraint.
Lastly, I would start by getting use to not using nurbs for geometry and secondly getting use to making controls as well. Look up "Zeth Willie Double transforms", it will help a lot without a doubt!
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