I had a similar issue. What I did to fix it was to trick the computer.
If you have the same issue as I did, the Matrixbrute thinks it is in tune.
Take a CV output from something, let's say osc 1 supersaw and input the CV into the osc pitch "CV in" to push the osc that is -1 semitone down -1 semitone further.
Press hold note, hit a note, then run the autotune sequence. You'll hear the oscillators moving around to find tune. If all goes well, when tuning is done, remove the CV Jack's and all should be in tune.
Goodluck!