Is there an obvious reason for traffic from a MiktroTik AP with source MAC address 00:00:00:00:00:00 ?
We have two APs connected to a Cisco switch, and it is continously logging this message:

%SW_MATM-4-MACFLAP_NOTIF: Host 0000.0000.0000 in vlan 44 is flapping between port Fa0/19 and port Fa0/17

I think it means that the two APs connected on port 17 and 19 are both sending traffic from 00:00:00:00:00:00 and the switch is updating its MAC address table all the time.

I have tried to trace the traffic using Tools->Packet Sniffer, but unfortunately it appears to be impossible to match on that MAC address. The all-zeroes value is probably used to turn off the MAC address filter?

I wonder what kind of traffic it is, and if anything can be done to select a different MAC address or turn off the traffic.

Do you have WDS enabled on both AP's?
This should help .

Also - you could create a MAC filter and block the 00:00.... and see WHAT stops

No there is no WDS. The two AP's are for different directions (sector).
As I wrote, it does not appear to be possible to select 00:00:00:00:00:00 as this probably is used as "do not filter on MAC".