My 3.5 month old baby boy cries for no reason?

I know this isn't colic as my daughter had this and nothing soothes a colicky baby. also colic pes by about 12 weeks. He cries so much and so hard but is instantly soothed when I pick him up. The doctor thought he had acid reflux around a month so he takes axid twice a day. Is it possible this has stopped working and its the reflux. He spits up ALOT and its generally very watery with milky bits in it. By the way he is bottle fed using milk only that I express. Could it be anything to do with the milk? If it is not the reflux and mearly that he wants picking up, can I leave him to cry. I have a vague memory about not letting baby boys scream as it can damage their little private's, but can't remember for sure. Thanks any advise will be greatly appreciated.