Not sure if this helps anyone, but just in case it does.
I just got a Microbrute and Beatstep this weekend and was excited about playing with the CV functions of the two. I was initially frustrated when I tried to hook the two of them together, as I experienced the three octave behavior noted here. I did some testing and at least got a suitable workaround. These are just my observations.
It's important to note that the "Pitch" function on the mod matrix is not an "objective" CV input. Its output is tied to the keyboard of the Microbrute. The initial relative pitch of your sequence coming in to the Microbrute from the Beatstep can therefore be affected by it.
If the Microbrute is powered up with the Beatstep already on and connected, my sequences will start in a low register. The second I hit a key, however, the pitch gets shifted way up. From this observation, my guess is that it has an initial default power-up setting, but after that, it is responding to the last key pressed (and actually apparently playing a note three octaves above that).
My process is to either power-up with the Beatstep on and connected (and not touch the keyboard) OR start with the Beatstep "pitch" input unplugged, shift the octave down three octaves (you can do three octaves even though it looks like it might only do two) and then play the lowest C on the keyboard. Then, plug the CV out of the Beatstep into the "Pitch" in of the mod matrix. The pitch should be shifted down now, because it is basing everything on the last note played.
You can also play any key while the sequencer is playing and hear the shift, but note that the octave shift will only occur in the sequence if you hit a key after shifting the octave down (just pushing the octave +/- keys doesn't do anything).
This may be really obvious to most of you, but I thought it might help someone.