I have tried this a few times now. If I leave in the middle of a kerbal planting a flag and go to the map or return to the space center I am then unable to left click anything other than the items on the ESC/Pause menu. I can pan and tilt with the right mouse button at the space center but cannot get any buildings to select. Also if I quit to the main menu no menu items highlight. I have only been able to get out of it by reverting to an earlier save. I imagine that the flag dialogue must be messing something up waiting for me to enter text, but it never displays again. Long story short, don't interrupt the flag planting.
