So I'm driving to Trail Jeeps today and notice the rattling from the roof rack is way louder than usual. I pull over to inspect and the washer/nut on the right side in the rear is gone. !!!  So I drove it real slow the rest of the way and Wes hooked me up with a new washer and nylon inserted nut. Thanks Wes! 
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There's always been a bit of rattle from the roof rack but I assumed that was standard. Now I'm pretty sure that nut was probably loose the whole time, slowly working it's way off. It finally falling off completely may have been a good thing as now it seems to be much quieter going over bumps. 
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http://wayalife.com/showthread.php?p=621404