If the problem was there before you replaced the 3 port valve, and you have confirmed that the new valve is working OK, then it is not plumbed in correctly.
Seen it many times - plumbers are great at connecting pipes together but not so good at working out the logic. (No disrespect to plumbers)
So my reckoning is the pipework is not routed correctly.
It could possibly be that the valve is working in the wrong way. I.e. it is electrically wired incorrectly to the controller.
Honeywell do a pretty good data sheet for the electrical side. Pipework you'll have to trace out yourself.
Unliely to be the controller.
As a long shot, unlikely given your question and info, you may have a bit of crap in the new valve which is stopping it closing properly.