No doubt could be a software issue but please be aware that a intermittent or high resistance connection in zone wiring could easily mimic a software problem. Don't know if you have ever checked how the wires are connected at any of your zone actuators, but if the wires are just twisted together or speed nutted, this is very bad news in general. Twisted copper in a low voltage (24v) circuit exposed to wide temp and moisture extremes is just asking for connection problems over time. Over the years dealing with various zone connections and cut wiring on my system I always solder the wires back together. Provides zero volt drop connection and eliminates problems further down the road.
