I can't help with the issue, but just as a note the STP change is a consequence of the port flap, not the other way around. You see the port go from 1Gbps Full Duplex to down, and STP responds by moving the port from designated to disabled. If you can fix the port flap the STP change will likely go away.
What is causing the flap is just a case of eliminating the variables. Check the cables, reboot the WAP, if you've got a spare port on the switch try that, and if all that fails, as Meraki support said, reset the WAP.
Did anything change when this started happening? MS firmware upgrade, MR firmware upgrade? Adding a new MR to the switch? (maybe taking it over the PoE budget).