Rob10, I think I agree. I updated to the latest firmware and after a few calibrations, windows restarts, tinkering (the default pedal settings did it!) and a windows calibration (which allegedly I shouldn't use) finally I got them to behave. All zeros and although the bars for wheel brakes jump to the middle in the axis control section, inside the mission they seem to be working properly.
I have done a DCS repair this morning, btw. The rudder pedals have been working fine for more than a couple of years now, so I looked at the latest change which was the update.
Anyway, thank you everybody that paid attention to my issue.