Multi-Monitor issues after the last update

So I use a Macbook Pro and have it connected to a Apple Thunderbolt display through one prot and to a standard monitor to another. So with the laptop I have three screens.
I am running windows and MacOS and flicking between them both seamlessly although but as a rule I will be running the Thunderbolt display in Windows and the other two displays in Mac OS.
Up to now the three screens have been seen by both Mac OS and windows without an issue.
After the last update I noticed that the macbook and standard monitor didn't have win OS desktops. IE I could not swipe left or right and move between win and mac OS

To cut a long story short what is happening is that when I connect the three monitors instead of the windows desktop appearing on each monitor I get three instances of the windows desktop running in the thunderbolt display. I only see this when I hit the F3 Mission Control and then see the 3 windows desktops on the same monitor. Obviously I can swipe left and right and cycle through the three windows desktops on the thunderbolt display. To solve it I can then drag them to the right monitors and all is good fir a while. Until the laptop goes to sleep and then when I wake it up they have all jumped back to the Thunderbolt monitor, just the windows desktops, the Mac desktops all stay where they should.

A note that may be relevant. In windows I would set the Thunderbolt monitor to be the main display (the one that has the icons on it). This works fine until I wake the system back up. Then the windows main display has jumped back to the macbook.

Its making the system extremely hard if not impossible to use. I have done all the normal things like booting the windows and mac OS up and down and reconnecting the monitors . I also run everything in full screen mode.