Ok, so tried a few more things:
The air can be purged out of all circuits if it is run with the boiler off. I can achieve silent flow whichever zones are open in this way.
If I fire the boiler, as soon as it reaches temperature (currently flow is set at 70C) I hear air bubbles coming out of the top of the boiler and through the pump.
If it is circulating through DHW or Auto Bypass Valve at the time, I get quite a large overshoot on the flow temperature (approx 8-10C) before the boiler modulates down. I am sure this is to be expected, as in either of these scenarios, the return temp is higher. But I guess it might explain why the noise is worse after either of these circuits have been active.
Thoughts?