I would totally look into SLEEP APNEA. I think the reflux may block his airways because it comes all the way up and then he stops breathing. It looks like his breathing get much shallower right before he wakes up (look at his tummy).
I have read a lot about sleep apnea from englarged tonsils and adenoids which are not unusual in reflux babies. My son got his tonsils and adenoids out when he turned three…If I would have known how much it would have changed him for the better – I would have taken them out at Justice’s age. I would get a sleep study done FOR SURE. I don’t think he is startled from a dream, or the movement of the bed….One other refluxer I know just got a sleep study and it turned out that he was having 6 episodes an hour. Both our babies never napped during the day and always had to “cry it out” to fall asleep. Oh, and my son has never had one ear infection.
Enlarged tonsils
Enlarged adenoids, which can block the nasal airway, may also be attributable to EER in very young children. In a study of children less than 2 years old who underwent surgery for removal of enlarged adenoids, 42% also had a GERD diagnosis. By contrast, GERD was diagnosed in only 7% of a control group of children getting surgery for insertion of ear tubes but whose adenoids were normal. The association between reflux and adenoid enlargement was even stronger in children age 1 or less. In this age group, 88% of those requiring adenoidectomy had a GERD diagnosis, whereas only 14% of the control group getting ear tubes had a GERD diagnosis (21).
http://www.marci-kids.com/eerpharynx.html