Ok, got it to do it again, where you see I'm in boresight mode, if you look at the elevation position on the radar screen, it is depressed, and the azimuth position is not searching left and right when this is happening.
You should also see the elevation flicking between depressed and the correct position, this is when I am using my warthog and the workaround I found (holding TMS down)
Using either my TM MFD button, or clicking the button in the virtual cockpit doesn't trigger this, only when using my Warthog, and the TMS buttons are not mapped via the TARGET GUI, they're just using the directX inputs in the game itself.
The issue plays back on my install.
Track file... F-16 boresight issue.trk