Yup,
There is a process that I do to fix this issue.
1) Creat icons/control curves(nurbs preferably, polys require other settings). Vert snap to the root that it will control.
2)Scale as needed to shape and shape(you can position it further by switching to component node if needed as this adjustment will not affect the actual pivot point).
3)Select the control(icon shape you just created), and shift select the joint.
4) Hit 'P' to parent.
5) Press control G two times.
6) Shift 'P' to unparent
7) Name the new "pads" and control to your own naming conventions(mine is jointname_trashpad, and jointname_cleanpad, jointname_ctrl).
8) Now this is important!!!!! You should not have frozen transforms, and don't do it yet. You want to go to your rotates on the CONTROL, not the pads, and enter '0' for all the rotates only. You will see your control/icon snap to the proper orientation of your joint.
9) NOW you can freeze transforms to get rid of translates and scale information.
10) Lastly, this depends on how your control is controlling your joint, in this case like the fingers, I would grab my new control(not the pads!), shift select the joint and "orient constraint".
This should take care of any visual orientations that are messed up. However, the cleanpads now give you controls in which to add attributes and make it easier to animate because now the control has no transforms, only the trashpad will hold those values .
If you are still having issues, let me know!