I would not try to use those port pins as they are connected to the microphone input circuit. Why don’t you use the switches that are provided on the board (connected to P1.0 and P1.1)?
That being said, the only reason I can see that P6IN should return those values when only P6.0 is an input is that P6OUT must contain something other than zero. Try writing zero to P6OUT and see if that helps.
Another thing that you might try is that the standard way to test the logic level of a pin would be something like this: