I am not sure what is the cause, but I know that the mappings I set do not hold from one session to the next. Whether it is a bug, a failing controller, or a faulty USB hub I cannot discover. The mapping that I set will work while I am playing, but once I log out the same mappings might change to any one of the many controller buttons.
EDIT: Just had to remove control manager (I think). I tried to turn on and off several devices that I change from time to time. After removing CH Control Manager the mappings seem to be holding.