Not much of an answer, but I found this on an FAQ page from the University of Missouri Kansas City's web site:

A person holding more than one degree wears the gown and hood of the highest degree. Someone having two degrees of equal importance can have the velvet border of his hood indicate both colors, but usually the last degree taken is the one indicated by the colors of the velvet. The color or colors of only one institution may be shown in the hood lining.
-- http://www.umkc.edu/commencement/exp...nofregalia.asp

That being said, you might wish to consult with both institutions to see if they have a particular protocol regarding this situation.

regards,

Todd