This problem seems to randomly happen if I hit IWT again when my guys get close to the NPC. I don't think I've had it happen if I don't do that. Like doing that makes the game think the window *is* open for some reason when it's not, or something. Like Littleburst says, my workaround is to interact with another NPC and then go back, but moving far enough away that the window would normally close should also work.