The mould is most likely to be caused my condensation which is rising as humidity from the main living area. As humidity is relative, warm air will hold water, and cold air will not. Therefore as the humid air reaches the loft space then the water within the air will be released and condense on the roof timbers. The best way forward is to ensure that the humidity within the main living areas remain at an acceptable level by the correct use of ventilation.
Peter Barber CSSW. CRDS
Make sure it's not dry rot ( ask the question on the Internet "how do I tell if I have dry rot") then put in some ventilation tiles above the insulation at the back and front of the house so you have a through flow of air.