Turns out the thing that was causing DPI issues, was an instanciation of a System.Windows.Forms.WebBrowser, comment out / remove that one control from one of our user controls and voila, all is well.
This answers my question, my issue is resolved. Although I'm still very curious to find out why this happens. (Don't ask me how many hours I've spent grasping at straws before finding this)
I Might add that while this has definitely proven to be the source of my issue, I have not been able to reproduce it in a smaller application.