How long has he been back on his acid reflux medicine? This sounds to me like his acid reflux is flaring back up. Many babies do not outgrow acid reflux until they're more like 12-15 months old. Also, acid reflux medicine will often take 1-2 weeks before it will start working again, because it has to first repair the area that has been affected by the acid backing up before your child will start to feel relief. While laying flat, the acid can start to creep up the esophagus, causing things to hurt.
It's always tough to determine when to take your baby off of the acid reflux medicine. It's almost deceptive, because your baby may seem fine, but the acid might be slowly deteriorating the throat lining again. Once he gets to the crying stage, it is sometimes because the throat is finally to that raw stage, and thus, nothing is left to help protect it from the acid.
You might check with his doctor and try putting him back on the acid reflux medicine (remember, it is not something that a one or two time dose will fix...he'll need a daily dose for probably 1-2 weeks before you'll start to notice a difference).