Why could they not just deduce that this was the problem? It must be very complicated from a troubleshooting point of view. Just my opinion.
Part of the problem may be that a loose cable is in an uncertain state. You were previously counting on the idea that "the timing-chain that timestamped all the particles" is in the same as "the timing-chain that we spent months checking delays in". Maybe the cable was tight during datataking and loose during the time-delay calibration, or maybe it was loose the whole time.