5 month has had nightmares since birth any way to stop them?

My 5 month old is still having these weird nightmares. He has had them pretty much since birth. It starts with a little wimpering then goes to that hiccup type breathing , like hes been crying alot but hasn't. Usually I come in then and see what I can do. If he starts acting like its a serios nightmare I try to wake him up but even when Im gently shaking him and trying to wake him up telling him hes ok we are here, he stays in it in like a limbo mode for at least 1-2 mins scaring the heck out of me. And believe me I couldn't do more to wake him with out hurting him I try so hard to wake him up out of it. Finally he opens his eyes wider and you can tell he is out of the dream and looking around. He does have digestive problems and has a seriosly hard time taking naps during the day, maybe 3-4 10 min naps. But then goes down for at least 10 hours. The only research Ive found is that its a early sign of mental problems. I pray thats not it. If anyone has advice it would be great. Thanks