for multiple AP sites we almost always use CMM’s. for a single AP we usually stick to a sync cable. you may want to redo the sync cable or at least check it as a faulty sync cable could cause the problems your seeing
I try to avoid passing sync through BH’s and SM’s unless it’s a micro-pop.
I would recommend adding a sync pipe at each location - it’s 99 bucks and will ensure solid sync at each tower.