Any change to any of the 3 app's Color Settings prefs would do it. Next time it happens check the Color Setting in each, if the settings name is Custom, that's the app that is out of sync.
I have not adjusted any of the individual app colour settings, if I open a document created by someone else that uses a different colour profile would this disrupt synchronisation?
if I open a document created by someone else that uses a different colour profile would this disrupt synchronisation?
No. Synchronizing Color Settings doesn't have any affect on existing documents unless they were created with no embedded profiles (the CM Policies set to Off), in that case the Color Setting's Working Space is used to color mange the doc. If a doc has profile assignments the Color Setting's Working profiles are ignored, not changed.
A change to AcrobatPro's Color Management preference would do it, or if you are having problems and trash the general preferences, Color Settings would be set to the default. A seemingly minor change like checking one of the Ask... boxes, or one of Photoshop's Advanced Controls, would also do it.
When it happens find the app with Settings set as Custom and you should see a mismatch.
Ideal, I will monitor over the next few days/weeks and follow your advice in the event. If I find anything or get to the bottom of it I will post my results here for the benefit of others.