The issue is the last bus to be started is the only one which may be read or written.
When I query the MPR121s on bus A and bus B the values for both buses will only return the bus which was started last. So if I start bus A first and bus B second I will only get values on bus B when I try reading both buses. If I swap the order of setup and start bus B first and bus A second then the values returned for queries on bus A and bus B will only be the values on bus A. I confirmed the hardware output is on the last started bus only using a scope.
Thanks for the help.