It does make sense, and further suggests that your programmer and 3-port motorised valve are working correctly. A brief description of the operation of your CH system, with diagrams, may make things clearer.
If the programmer's power supply was interrupted, the initial state of your system will be like this:
The motorised valve's return spring will have moved the valve to its resting position (DHW only).
If the programmer first calls for DHW the pump/boiler will be energised via the cylinder stat (the path of the electric current is indicated in Red):
The motorised valve will remain in its resting position because no power has been supplied to its motor. In this position the valve only supplies hot water to the cylinder.
If the programmer now calls for CH, as well as DHW, 240 volts is applied to the valve's motor via the room thermostat:
The motor advances the valve towards its mid position.
When the valve reaches mid position, its first micro-switch (the upper switch in the diagram) toggles over:
Now the valve's motor is no longer powered directly from a 240 volt supply. Instead, it receives its power via a 13k0 resister and a diode. The resultant reduced power is insufficient for the motor to advance the valve any further, but is just sufficient to prevent the return spring pulling the valve back to its resting position. So the valve remains in its mid position, supplying hot water to both the cylinder and radiators.
When the cylinder stat is satisfied, it toggles over:
Besides applying 240 volts directly to the valves motor, enabling it to advance the valve beyond the mid position, this switching action also removes the power supply to the pump/boiler. This is the reason why you noticed the pump go off momentarily (the third item in your posting).
As the valve moves further across, it toggles the second micro-switch. Thereby, restoring power to the pump/boiler:
The valve continues to move across until it hits the end stop - stalling the motor. In this position the valve only supplies hot water to the radiators.
When the programmer stops calling for CH and DHW, the valve remains in the fully across position because its motor is still directly powered - this time from the programmer's DHW Off terminal:
If the supply is not interrupted then, when the programmer next calls for CH and DHW, the pump/boiler will be initially energised via both the room and cylinder stats. This is because the motorised valve will still be in the fully across position (it takes a few seconds for the return spring to move the valve to back to the mid position):
This is the point at which your fuse blows.
Hope this helps,
John