For a specific reason, I need to have either the DVI-I or DVI-D port as the primary, and the Display port as the secondary.
No matter which combination I try, the selection works during POST, but after Windows starts it always reverts to Display port as the primary.
Checking the Intel Windows graphics driver config suggests that this should not be happening, as the presented layout is what I'm after, but regardless, the actual allocation of Primary and Secondary video is wrong.
This is really frustrating.
This is due to the way that Windows queries the physical devices. I've seen the same issue with SSDs and HDDs wherein I wanted to see SSDs as Drive 0 in Windows.
Actually, drives ordering depends on PCI bus scan ordering by Windows kernel (which depends of platform and mostly hidden) and storage controllers drivers boot ordering, i.e. the first controller driver loaded will first offer its controller-connected drives for OS.
I would be surprised if you aren't seeing something similar.
Do you have the option to disable some of the video outputs?