Ok, since there was a lot of people having issues with their sync I did some in depth research.
First, I want to adress, that there have been discussions about the Sync Clock settings in the MMC and that 24ppq would be advisable. I am preeeety sure that this value is ONLY relevant, when you are using the CV clock in as a clock source, which as far as I can tell none of the folks experiencing trouble where. I am sure DrJustice could confirm this, because he is a wizard, but I also just ran a lot of very detailed test and REGARDLESS of the Sync Clock In settings my MatrixBrute shows about 3 to 4 ms worth of fluctuations at 96 BpM when the sequencer is running, synced to my CuBase 10 pro with an RME Babyface.
And here we get to the bad part:
This fluctuation is present in any setting I could conceive. I tried USBMidi, Midi via DinJack, various MMC settings, differing buffer sizes for my interface (down to 2ms latency on 64 samples)....
Which is to say, I am afraid it is an inherent property, if not to say flaw, of the MatrixBrute. I hope I am overlooking something, though. Please feel free to prove me wrong.
When I find the time I will test one more time with an MPCLive as clock source, and I will report those results as well.
And if you think, 3 to 4ms at 96 BpM fluctuation is not that bad: I only started this rather tedious operation, because I was not happy with the sync musically before...