12 month old been on milk a month, got stomach virus, now cant keep milk down.?

ok, need to know if any mommies out there have had this issue... or any one in the medical field knows. My son had been having some cows milk for about a month then he got that lovely stomach virus that is going around. they said no milk (i still feed him when going down to sleep, 3 x a day). so when I reintroduced it he didn't really want it. I can get him to drink some after dinner but then he throws it up about 45 minutes later. I thought something was wrong with the milk but have tried 3 different jugs. he eats all regular food now and eats it just fine. I called the dr and they said he might be allergic to it and to try soy. I said he had been drinking it for over a month just fine! they said it might be a delayed reaction... so I really feel that is not the case, just doesn't sound right. i feel that he may just need like a week off of the milk and then try again, maybe his tummy is still week from being sick and needs to get stronger. any suggestions??