After mirroring your joints did you freeze transformation on them and then orient them? This should be done before binding to clean up any bad rotations and zero out everything.
How are you connecting your controls to the joints, probably an orient constraint?
If so then another way (which is my prefered way) is to attach a control curve by parenting the shape node to the joint (for FK). To do this create a nurbs circle (or what ever control you want) and use
`parent -r -s curveShape Joint`, where curveShape is the shape node of your control and Joint is your joint name. This parents just the shape node and so it becomes the joint itself. When you select the curve control you are really selecting the joint itself.

Richard