.... seams as the engine takes it ....
your engine makes the heat :-? 
i know that but when its cold out side the inside is cold and pipes to rad inside are luke warm and engine pipes are hot. but rest of year all hot.
sounds to me like the Heater bypass valve is plumbed in the wrong way around!
do this ckeck - set the heaters to full heat and start up from cold. If the matrix is getting luke warm then it is not getting hot water flow - you can check this by feeling the heater matrix pipes in the footwell area
now turn the heater controls to max cold setting - if the matrix pipes turn hot then that's your answer
the point is the HBV should divert flow from the matrix when tem controls are set to fully cold.
If at some point in the car's history, the plumbing of the valve has been disturbed or indeed the valve has failed - you could get this problem
IMO the electic water pump is not this issue or solution. my heater works broadly the same whether the electric pump is running or not