What # circ on the boiler to boiler? 007? Flow checks usually hold well, but if the flow characteristics in that loop are powerful enough, you know the deal.....you risk a terrorist attack from within your home!!!
I assume you screwed the stems back in all the way on the checks.....try to put a long screwdriver up against the flow checks, then to your ear, and see if you can detect movement. Try with the circ on and circ off. (you have already I think)
This 'fringe' weather makes it tough on controlling the temps. Was this an issue in the past?
Obviously zone valves are positive closure, but still you should be able to control the 'ghost flow'.