My 3 mo old baby wakes up very hour due to congestion any ideas why and how I can help him? ?

He does not have a cold and no other symptoms. He is not at all congested during the day. I have tried raising the head of his cradle, humidifier, vicks and saline drops, leaving the window open a crack for fresh air and everything I can think of. As soon as I sit him up the congestion goes away. Sleeping propped right up with a pillow works but only for a few hours. I don't think its an allergy as we have no pets, no smoking, no carpet and a well cleaned bedroom. Help!!!