I've had that happen too and I think I found out why: After you set the parking brake after pushback (as told so) the ground handler comes walking a bit closer for like 3 seconds. IF you hit "confirm good engine start" BEFORE he arrived and stopped at his new position, it will bug out. So the solution would be to only click "configm good engine start" AFTER he has stopped again close to the nose of your aircraft (you can still see him).
Does this help you? If yes, than it's a workaround for that bug.