OK, so you can forget what I said about S-Plan - 'cos you've got a Y-Plan system.
Remind me again. Was it all working ok - and suddenly started doing this without anything having been touched/changed?
The only other possible explanation I can offer is this:
Assuming that the boiler controls the pump, in order to provide pump over-run, the boiler will have a permanent live and a switched live wire connected to it. The permanent live is - like it says - live all the time regardless of what the programmer, thermostat and valve are doing. The switched live is controlled by the programmer and/or valve (depending on mode) and should only be live when there's a demand for heat.
It seems to me that the switched live has somehow got itself connected to the permanent live - maybe a short somewhere or a component failure. This could be in the external wiring or within the boiler itself.
So you need to identify the switched live wire, and disconnect it from the boiler. If the boiler and pump *still* run, the fault has to be inside the boiler. If it doesn't, it's an external problem - and you need to find out why this wire is live when it shouldn't be.