Yes, a course of antibiotics can definitely mess with your digestive system. I took six weeks of antibiotics back last May for a sinus infection, and while I really don't have severe heartburn, I do have other symptoms including bloating, shortness of breath, tightness in my chest, lump-in-throat sensation, and incessant belching. I'm STILL not back to normal!
I do better when I stick to a regimen of probiotics (yogurt, acidophilus) and make sure to get a lot of fiber in my diet.
You can read my previous posts for the continuing saga. My theory is that the antibiotics wiped out both the bad bacteria AND the good bacteria from my system, and it takes quite a while to regenerate the good bacteria.
In my case, I had scopes from both ends and was fortunate enough to have a finding of "normal." No ulcer, no h pylori, no esophageal damage, not even a hernia. I'm sure I'd feel better if I'd lose my excess weight though.
Hope your symptoms dissipate soon. It's nice to have people on this board to commiserate!