Hi, C. --
I'd definitely suspect the vitamins before even any changes related to your mini pill, though I am no doctor. I, myself, have had reactions to different vitamins, depending on whether I had them on an empty stomach or with food -- or in different combinations. Maybe the vitamins are just more advanced than his digestive system can manage.
My daughter had reflux from birth, and she had a terrible time with it. Even now, if she gets worked up, she will reflux, and she's 3. We used an Amby Baby hammock instead of a crib from the time she was 1 month old, and it was the best thing we EVER invested in. It's such a wonderful device - to cradle, rock, comfort and support the baby, and it holds them with their head gently elevated so reflux becomes a non-issue, at least while sleeping. Check out www.ambybaby.com. I would have sold everything else I had for my daughter to have been able to buy this - it was THAT significant for us, and it abides by the latest guidelines re: SIDS.
My daughter's pediatrician prescribed reflux medication for her, and that helped. I think Soy or milk products could also be culprits, but it would seem strange for them to manifest now vs. earlier, I'd think. Again, I'm no pro -- just a mom with a refluxing kid.
Good luck!
H.