How old is the baby? Have you considered reflux? There are babies suffer from something called “silent reflux” and the food is irritating their esophagus without actually coming back up. It is best to keep them propped up for a period of time after feeding just to make sure the food stays down in the stomach. There are times when medication is needed (Zantac, Prilosec for example). These are all avenues you should explore in addition to the formula issue.
What makes you suspicious that it is an allergy?