I have recently been diagnosed with celiac, so no wheat flour whatsoever.  Also, I am allergic to corn....  I have read that arrowroot would not work in a roux; it is not just the thickening I want, but that flavor that a well browned roux has.  Any alternatives? 
Alex and Aki at "Ideas in Food" have developed a gluten free flour that works as a substitute for wheat flour in almost any situation. I have used it successfully in a roux.  http://blog.ideasinfood.com/ideas_in_food/2012/02/what-iif-flour.html 