I have had a few problems when flying with additional windows open/imported in FI.
Say I have 3 windows open in the cockpit, in this case:
Radar Contact 4 - FSUIPC window
Speed bugs window from MD82
PDF reader showing charts
Sometimes one of the windows will suddenly reduce in size, so that only the buttons to resize/move/magnify are left. At the same time the P3D window on the desktop will minimise. When you maximise the P3D window on the desktop, it now has one of the open windows flashing within the P3D desktop window (normally the desktop view does not show the imported windows in P3D) and the view on the desktop window no longer follows my Oculus. It is in a fixed position!