Hi Marko,
It looks like the simulation code that you posted is assuming that the input to the WidebandCollector is modulated, because the ModulatedInput property is set to true.
However, I think when you collect real data using your microphones, the data is unmodulated, meaning it is directly proportional to the raw voltage. It is possible that the phased.SubbandMVDRBeamformer just doesn't work with unmodulated data - there are no documented examples showing it being used with unmodulated data.
I would reccomend going to the Phased Array System Toolbox Beamformer documentation page, and browing the Wideband Beamformers:
Some of these beamformers are documented to work with unmodulated data, such as the FrostBeamformer, GSCBeamformer, or TimeDelay beamformers.
https://www.mathworks.com/help/phased/ref/phased.frostbeamformer-system-object.html
https://www.mathworks.com/help/phased/ref/phased.timedelaylcmvbeamformer-system-object.html
I would recommend getting the simulation working if you set the ModulatedData property on the WidebandBeamformer to false to more closely match your setup, and then experimenting with some of those other beamformers that are documented to work with unmodulated data.
Best,
George