Went back and did all the finetuning and settings to optimise the sync.
I found i was using midi for note info and usb for clock, which is said in the manual as not a good thing, set both via midi clock.
I offset the device latency by 8ms (currently the i/o latency of my computer is set at 7.5 ms so that makes sense) and midi clock latency by 68 ms.
Now the sequencer syncs fine, but the arp was still strange: it does seem to get the tempo right, but only after one bar of playing. starting the clock earlier does not change this.
i think i fixed this by changing the setting on the input channel of the pro3 from 'clock' to no input. Strangely this clock input was not armed, so it shouldn't really have an effect at all. But now the arp starts correctly from the first bar?
So it seems like the problem was more to do with ableton live/ or the compatibility of Live and DSI.
So far so good, we'll see how it holds up.