I was, not to long ago, wiring up 60 Ethernet cables of which one end was chopped by previous owners so I had to trace the cables from the wall and correctly wire it all to a patch panel.
ANYWAY . . . I found what some of the sockets on the walls were faulty. The connections between pins 1 and 2 were open-circuit.
What if in the Ethernet socket of either the MBL or the AirPort there a connection is not correctly made and as such the it all falls back to 100 Mbps?