Naturally the MicroBrute is set to retrig the SEQ on each note, so it should start each note totally in time.
Well, my MB does not retrigger its sequencer on each note. I mean, it does retrigger a sequence but not the sequencer tick phase. It (the phase) remains the same from the moment I turn on the power on MB no matter if I press keyboard, play/stop seq, tap TAP button,... It may be off, say for a quarter, and when MB receives new MIDI clock, it's still quarter off, so MB registers external clock allright. But there is no mechanism to retrigger sequencer exactly on phase other than turn-off and on the machine and hope you hit it the right time (or start everything else in your MIDI setup according to MB).
I can't reproduce your situation, I admit, I didn't even try. If I understand it correctly: you are sending midi note-on messages from your DAW to MB, which is playing its sequence? What is the tempo of your DAW sequence? The same as MB's sequencer? And MB clock is midi synced to DAW? Or are you running them idependently and you are comparing / measuring MB SEQ's accuracy in relation to DAW's?
And yes, where is Arturia? At least some sort of problem confirmation (is this a bug on some of the devices or an awkward feature of the machine) would calm my turmoil
Again, future firmware request: Make it so that when the sequencer is retriggered under external midi clock, the seq's phase is retriggered, too (that's a normal behavior of my other synth's seqs and arps).