So the mv and c are supplying power to the transformer/relay and out of it, but the pump won't start until the relay is forced.
I'm thinking the relay contacts are oxidized, and need to be cleaned. When they have oxidation, current goes up, and voltage might appear ok. If any start capacitors are in the circuit, they can be faulty, breaking down under a load, while reading ok. I haven't heard of any caps in these systems, but just in case.
The following blog may help you- it's about different controller situations:
Hunter's website has some things to check concerning the controller:
Looks like it could be microprocessor lockup. It's quite a process, but here's what they say is the fix:
Good luck, hope this helps, and thanks for using FixYa.