I’ve had similar issues with passport photos - though less painful as it was just me, not me with a squiming kid. I’m crosseyed which isn’t all that obvious in photos unless you’re the passport office. After several attempts, we ended up with a photo where my right eye miraculously wandered to be pointed along with the left. Of course, that hardly ever happens and thus doesn’t really look like me - but I’ve been let in and out of a few countries now, so I guess it’s alright.
Good luck!