Yes, port 1 is the master (when configured with the 6.40 firmware). I don’t think there is that distinction any more in the RC firmware.
It is quite unexpected that the port 1 LED should behave any differently to the rest of the switch link lights. (It is as if they are using for the CPU port activity).
Thanks for explaining that this is normal behaviour. (Although I don’t think it is “correct” behaviour).