Hello,
Just some thoughts.
I don't have MicroFreak. But afaik then "Normal" polyphonic aftertouch and MPE is'nt the same.
Are you sure the presets you have tried have aftertouch modulation applied at all?
I don't have a MPE controller, so i can't test.
Does it work when you use standalone applications? In that case have you enabled MPE in your DAW, if it has to be enabled?
If MPE aftertouch really does'nt work poæyphonicly, then i suggest you contact Arturia support.