Over DuBois' tenure, the office been criticized for failing to address one of the core issues around government funded programs run by religious organizations--that of faith-based hiring and firing. A 2012 report left "critical questions unanswered" about how the government could work with religious groups within the limits established by the First Amendment.
MORE: http://www.washingtonpost.com/blogs/under-god/post/obama-advisor-joshua-dubois-to-leave-office-of-faith-based-and-neighborhood-partnerships/2013/02/07/52baa3aa-7131-11e2-ac36-3d8d9dcaa2e2_blog.html
See also...
Bush's director of faith-based initiatives praises liberal successor
http://www.salon.com/2013/02/05/former_bush_director_of_faith_based_initiative_extols_liberal_successor_partne/
