My 3 month old son is having diarrhea?

My 3 month old son is having diarrhea.He is bottle fed and has always been.He is on soy formula because at birth regular formal made him throw up because he could not handle the cows milk.He has been having diarrhea for 21 days now....This all started after he got his 2 month immunizations.I took him to the doctors and she did a culture which came back fine.So then she put my son on a new formula called Alimentum, she said I would notice a change within 24 hours....Well It changed the color of his diarrhea but did not stop it.So I took him to the ER to get a second opinion and that doctor told me its 100% normal to have diarrhea and he will not have normal stool until he starts eating solid foods,but what I don't get is that my son was having normal bms up until he got his immunizations so for 2 months he was fine and then all of a sudden he has diarrhea? I'm worried about him getting dehydrated so Ive been giving him pedialyte every so often throughout the day.I don't feel as though my sons doctor really is doing much of anything to help.No one should have diarrhea for that long and it be "normal". The only thing is that I cant change doctors because My husband is in the Air Force and we are stationed on base so my son has to see an on base doctor because of our insurance,so changing Doctors is out of the picture.I'm just confused and need some help I'm a first time mother and I'm worried about my son..please if anyone has any advice I'm open to it I just want my son to get better. I have tried all I can do!