How do you fix intermittent heating problem?

I have a new Salus programmable thermostat (RT500RF) and a new Bosch Worcester Greenstar 24Ri boiler.
Sometimes the thermostat sends a message (flame indicator comes on) but the boiler doesn't get it so doesn't put the boiler on for the rads. (Bosch came out on an occasion it wasn't working and said the boiler was only getting 103 volts from the stat so it wasn't a boiler problem). When the installer comes out, it of course is working so he is wondering should he go back to wired thermostat or change the 3 way valve but we're clutching at straws.
When its not sending the right voltage the only way to get the heating on is to force the hot water to come on at the programmer.
Anybody met this before ?