The problem is the pump on the end of the manifold has a thermal cut out and this is triggered when a limited amount of heat is being used by the underfloor heating (UFH), for example only one heating loop is in use. When limited heat is being used by the UFH manifold the heat coming from the boiler may become too much for the manifold and this causes the manifold pump to lock out due to a thermal cut out in the pump designed to protect the floor from overheating. The pump does not reset itself automatically when you only turn off the zones of underfloor heating, as the whole manifold has to cool down, and this is only achieved when you turn off all of the underfloor and radiator heating.
How to reset the pump
To do this, you need to reset the pump by turning the heating off to all radiator and UFH rooms for 30 minutes to allow the whole system to cool down. The temperature dial on the pump should now read <35°C. The underfloor heating should now work as usual.
To reduce the chance of the manifold pump locking out again and not coming on, you should reduce the temperature of the water coming from your boiler (which is usually a dial on the front of the boiler), and/or reduce the temperature of the water running round the underfloor heating circuit (with the TRV on the end of the manifold). We suggest this should be set to around 40ºC on the manifold TRV, as per JK's Quick Start Manual.