Yes i have had a very similar issue with my tripple monitor setup. One of the displays is connected to the default onboard intel card and the other two are connected to my GeForce card. When i wake up the machine from sleeping, sometimes the displays are correct, but many other times i show 4 displays in my display settings (right click - display settings) menu. I always have to click the detect button in order for it to go back to three displays.
Now if i forget and it shows 4 displays, some programs will open but they will never show up as open, its like they are locked behind the scene, very frustrating. So i just got in the habbit of checking the display settings after wake up every time.
Now i did contact both windows tech and also posted on several windows forums but to this day have not found a solution, and its been years.
My gut feeling tells me that since one is connected to the onboard card which boots first but is not the primary display, the system gets confused sometimes or one loads before another is actually active, something like that. So it adds a fake display to compensate. And yes the onboard card display uses displayport as well. I even tried it using the DVI connection, same thing.
I used to think it was displayfusion multi display software causing it but i tried it with it removed and still the same thing. So im thinking it has to be something regarding connections and booting order im thinking. I guess i could go into the config and set the GeForce to boot first but i just never did.