Oh, it looks like I read your original post wrong--my problems are in the wrist, while yours is in the shoulder. Sorry about that.

Anyway, when creating the arm joints, I position each of them by opening up the Joint Orient channels and using them to rotate the joints (without actually using the rotate channels), and when I mirror them, I use the option to mirror behavior rather than orientation. That way, when in FK mode, you can select, for example, both elbow joints and rotate them together. When you mirror orientation, the elbows bend in opposite directions, so mirroring behavior helps save a little time and feels a little more organized.

But...don't put too much stock into that--I'm going to see if changing the mirror options may help my problem, but it's quite a stretch.

But for your end, could you try to describe for me how you make your rigs and maybe I'll see if I can help you fix your problem for you.