Hmmm, just writing out loud, here.  The difference between organic flour and regular flour would be the fertilizer put on the crops, the pesticides and herbicides used during the growing season (if any), and the processing of the grain to flour.  These things shouldn't change the chemical make-up of the grain used to produce the flour, so I would venture a guess that it is unlikely your coworker could be allergic to the grain used to produce the flour.  It seems more likely to me that they are allergic to one of the other factors mentioned above (most likely the processing, as fertilizer and pesticides/herbicides should not be present after processing).