The hot water works correctly in all respects.
The Heating works correctly according to the room stat but it pays no attention to the timer / programmer.
The Control board and the boiler do not care and have no knowledge about why they're heating water - they are non judgmental - they heat water promiscuously.
The room stat is acting as an on/off switch for the boiler and takes no notice of the programmer.
Under normal conditions the room stat gets its power from the timer / programmer (are you sure that the timer / programmer is really off when you think it is?)
Assuming the timer programmer is behaving correctly -the Room thermostat MUST be finding power to turn the boiler on from somewhere - and the room thermostat is acting as an effective on/off control as it should.
There are two questions to answer -
Is the timer programmer doing the right thing?
If it is working correctly then where is the room stat finding power from so that the boiler fires up?
I am not a boiler person. My advice is worthless.
In some circumstances - I think the CH only condition - the call for gas comes into the boiler from the 3 way valve.
http://www.diyfaq.org.uk/plumbing/controls/midpositionvalve.htm
Good luck...
Peccavi
April 2013