Well where does this second (toilet) switch wiring loop connect to the Fan/light?
Since the light works correctly with the door switch you're OK up to the Fan/light combo......
In the fixture: The 'toilet' switch loop ......(Black and White to the switch)........for operating the FAN should be connected between the Black/Light connection and the Fan/Black connection.....be sure to re-mark the switch loop WHITE wire to BLACK.........
And of course there are no other wires that connect to that switch loop..........