The Light Transmittance and Transmission figures used in a Part L calculation come from separate locations in OpenBuildings Energy Simulator. The best resource to distinguish the difference between these is the Data Reflection Report.
Transmittance is entered is the Materials Manager glazing menu - if this type of glazing is used in the building then this will be displayed in the list of Window/Rooflight constructions as below:
The Transmission factor can be entered into Part L under the Miscellaneous > Additional Surface tab. Changing this will not affect the Window/Rooflight constructions above, but only the individual Window in that has been selected from the list of surfaces. This will then be displayed in the Zone (Room) properties, as below: