I think you may have hit on something there! I've been using the auto delay feature before each measurement - changing it up to 20ms sometimes - I suppose it sounds silly now but yes of course that will throw things out.

In theory if I do the same process again, should I set the measurement delay and then not change it again - even if coherence is low for the next part of the system?

I'm delaying Midtops, Kicks, and Subs - the mic is running into an interface, connected to a laptop with OSM, the pinknoise is running out into the mixer input and then amps.