I am also having problems,
It is almost like the relationship between 606 and beatstep is 3/2 out.
If on 24PPQ it is out by triplets, both with 606 as slave or master.
If i put the beatstep subdivisions into triplets then all works great, as i would expect it to work not in triplets.
But, that makes everything pretty difficult when I add my computer to the mix, as now my BPM of ableton is out by 2/3.
I am on firmware 2.01 btw.