There are many systems using the Honeywell valve they are shown on their web site C, Y, S, W etc. More information is required to give a good answer. But the three port mid position valve has about 3 micro switches although only one is shown in the diagram these switches going faulty often cause the symptoms you refer to but would normally include a thermostat I realize with TRV's the role of the thermostat has changed and is mainly used to stop cycling in the summer. Also the variable output boiler has also been designed for use with TRVs and does not work like the old boilers so to advise on use of thermostats without knowing the whole system would not be helpful.
If we assume that the motorised valve is only a two port version, then the most likely culprit is the motor or gearbox within the valve itself. This part is replaceable without draining down.
The timer of course could be responsible as could an electrical fault in the wiring to the valve in even within the valve itself.
The only way to test this is with an electrical tester and of course the components are all at mains voltage.
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