Well, can i ask was your son only coughing or did he seem to have stomach pain also? did he have diarrhea? My son has acid reflux, although we didnt know that until just recently through and endoscopy/colonscopy combo they did. For us, the medicine they gave us gave him severe pain so he just doesnt take any. If it happens again i would suggest trying Rice Milk.
However, with the acid reflux, i would try to make sure his bed is slighly elevated if its not already and I would not give him his milk right before bed. i would give it to him as the night gets closer and although him to move around afterwards to force it down his throat.
You can email me for further details if you feel that it could be something other than the acid reflux. We found out after a few months of milk that braeden was intolerant to milk and had some food allergies. FOr us, he would be restless at night, cry in his sleep, and as it got worse, cry inconsolably. Hopefully that isnt the case but something to watch out for.
Good luck!
PS. I am currently taking my son to a homeopathic doctor to help resolve some of these issues. Only just started but if you are interested I can let you know how it goes and pass the info along.