gime a screen shot with the rig and the hierarchy and a shot of the problem.
to host your images so you dont have to crunch them down so they are illegable.)
it sounds like a combination of things to me. what you have might be the orentation and the prefered angle. where setting the prefered angle might fix it for now your orentations will probibly bite you later when you animate.
(see attatched to check the orentations) X should be pointing to the next joint in the chain either Z or Y should be pointing directly to the side of your joint if this is messed up let me know I'll let you know how to fix it.