Hi there, no experience with Pro Tools but I’d had the same problem with other DAWs. There is some compensation that has to be set up by the user for the midi and audio to be tight with the grid timeline of the DAW. There’s actually two nested issues, audio latency and midi latency.
Audio latency has to be addressed first, there’s some adjustment to be done as far as where overdubs get placed on the timeline, they can be a little ahead or behind from when they were performed. The setup to calibrate it is to do a “loop back”, where you route an audio output back to an input, and play the metronome out of the output while you record the input. You zoom in on the recorded audio and see how the waveform of each metronome click match up with the timeline, and compensate for it in the global audio settings until it’s right on.
After the audio is coming in reliably on the timeline at the time it was performed, the midi latency can be addressed, by playing out a sequence that has been quantized to the grid and adjusting the global midi settings to compensate. Some DAWs you can set a different midi latency per midi port, so you may be able to set it just for the Matrixbrute midi port (if you are using the USB plug). You should be able to get it where the midi basically fires a little early, and by the time it gets through the system and makes a sound on the Matrixbrute, it is right in time with the song/grid. Same goes for the midi clock, the daw should send it a little ahead of time so that the sound the keyboard produced is right on time, rather than flammed.
It’s a subtle problem that I think affects a lot of musicians with hardware synths, the timing can be shifted easily by all of the variables in the computer system.
