When you give him the pacifier, does he get upset that its not the breast? Or does he suck contentedly?
If I've read right, sucking helps keep the food down, and so it is possible that it is silent reflux. I mention this because you didn't mention anything about spitting up. Does he arch his back, strain as if it were gas, toss his head a bit? How about fussing during or after eating? My daughter doesn't have the full classic sign of arching her back-- she kind of doubles over and strains as if she's constipated, however with all the straining she lets wind rip with the best of them, and I haven't been having too much of an issue burping her anymore, although that was a huge one when she was a few weeks old and that's why the doctors told me it was gas and to give her Ovol. My daughter doesn't spit up an obscene amount, however I can definitely hear "wet" burps, she has frequent hiccups (every day... sometimes more, sometimes less but every single day), she seems to be chewing on something and if I look in her mouth at those particular times, there is always BM spit up. She is constantly sneezing, coughs several times a day, and in the morning it sounds like she's congested.
When I went to a breastfeeding clinic the lactation consultant there said a 20-30 minute feed was sufficient (40min was the maximum she said to let it go) and then if she seemed still hungry to give her a pacifier. She had said this because my DD's desire to eat and to suckle are represented by the same cues, and of that she is totally right. She stuffs her fists in her mouth and shakes her head back and forth, rooting. lol.
Reflux is a tricky thing to deal with. And it seems trickier for doctors to diagnose for some reason. I've always felt my daughter had reflux, but the doctors just don't seem on board with it. I've cut back greatly on diary products and have noticed a difference, but she's still rather uncomfortable.