Updated graphics driver today, when I open maya the joints look perfect, but 3 sec after I open they go all crazy. I used the controls for the rig and everything still works and animates properly, the joints just do not display correctly.
As Ritthamus pointed out, this is a driver issue with nvidia. I found a temp fix though if you don't want to rollback. You choose the first joint in your joint hierarchy, and ctrl+a to get to your attribute editor while your joints are selected. Under display, make sure you check "Hide on playback", and it should fix it. You have to keep doing this for every bone set you make, and its kind of annoying to keep repeating the same task, so I just roll back the drivers as well.
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And, unrelated, but a driver rollback 100% did fix the problem. So, I guess I will wait on new drivers.