Ok, have found the issue with quest setting, and it is simple enough. Working out why things are as they are and avoiding resultant weird issues may be harder.
We reset all daily preferences in KoLmafia.resetCounters(). This is called in KoLmafia.refreshSession() if it's our first KoLmafia session of the day, but this happens after KoLmafia.refreshSessionData(), which updates quest log among many other things.
This means that on first login of the day, we are blanking out daily preferences in resetCounters() after setting them for things like quests, No Hat, Pantogram, Horsery, anything in Campground, etc.
We should certainly clear daily preferences before we start setting them !