New Carpet in effected room, new underlay? it could be that the underlay and Carpet have too high a TOG rating to allow the heat to penetrate through and heat the room! you are getting a flow rate through the circuit, so I don't see what else it could be!
What Model Camray 5 is this is a Combi per chance?? could be that the pump is stopping with the burner I've seen this a few times usually down to a failed auxillary switch in the diverter valve actuator
While you had it stripped down I assume that you checked for a Cold water supply to the boiler?? there is an appliance isolating valve which is tucked under the plate heat exchanger, near the filling loop is this valve on? I have had a blockage occur in the pipe work taking hot water from the...
It is not un-common for a Honeywell Programmer to fail in this way - even mine at home did this when I had to do some work elsewhere that involved switching the power off - new programmer should sort it!