I just updated and notice when you have Night Mode on with Flash on Auto, it doesn't use the flash to take pictures, even in dark room. It does use the flash in Night Portrait but not Night.
If I had to guess... in Night Mode the camera tweaks the settings enough that the camera believes it doesn't need the flash. In Night Portrait though... you are trying to illuminate a subject closer to the camera and the camera may opt to use the flash for better details in the portrait.