Late to the game and New MicroFreak owner, but I have been experiencing various similar issues loading presets from MCC to the MicroFreak.
I did figure out a solution that seems to work....so far....
If I open MCC and THEN plug in the Freak and THEN power it seems to be willing to play nice. This is not the prescribed order of operations stated in the MCC, but through trial and error it seems to have resolved the loading issue for me.
Hopefully this may help anybody else running into preset loading issues.
(Running os11.2.2 on a 2017 MacBook Air)