My 10 month old also has milk protein allergies and the other symptoms you mention have come back such as water eyes, etc.....first of all, we are seeing an allergist this week to see if we can try to get him off that stinkly Alimentum formula....secondly, from what I've learned over the past 6 months, ever consider that he has reflux? I say this as I understand when they sleep the food (formula in our case) can come back up and sit in their ears/sinuses and cause some of the issues you mentioned.... When I was first told this, I thought my doc was a little off as our son has not projectile refluxed in a while, but if it comes back up and sits, could cause a 18 month ear infection.....

Hope this helps,