I have a real problem with Maya 2012 joint tool when i try to create a joint chain the bones are not represented right, they are not connecting the joints they are actually oriented at a 90 degrees angle. I took different measures to fix it in vain.. Did a preferences reset by deleting the prefs folder and let Maya create a new one, but no luck. i think the tool is at its default settings but i can be wrong . to describe this better i am joining pics of how the joints are represented and a screen capture of my joint tool settings