My son has a cow's milk protein allergy and a soy intolerance, he is on a hypoallergenic formula and doing well. He was sick all the time (he's got reflux too though) and developed a very bad rash and wheeze (he had to have breathing treatments for a while).
It may be that your LO has an intolerance or a sensitivity. Definitely talk to his Dr. about trying another formula. Also, when we switched my son, the Dr said we may see some symptoms of the allergy for up to 2 weeks while all the protein clears his system so if you have recently switched, this could be the issue.
Also, remember he's very young still. Lots of babies that age don't settle very long at all.