I know it is hard to always have to schedule your workouts on an empty stomach, but I think it will be worth it. I didn't always have to do that, but as my reflux worsened, I found I could no longer work out after eating. Even an hour later isn't enough. Probably 2-3 hours would be fine.
I couldn't believe that even walking caused reflux after eating. My symptoms were mainly heartburn (severe at times) and breathing problems.
I had the Nissen Fundoplication surgery in February 2009. I'm very glad I did, because my lungs were in horrible condition because of reflux. The surgery has really made big difference. I'm having some issues now (it's a long story, but I was on steroids and coughing horribly after surgery, and it may have compromised my wrap...or, it could be too tight, and food is hanging out at the wrap site. Don't know...my lungs are still pretty good, but I'm getting a few symptoms, so I'm going to see a surgeon next week and discuss my issues. I'll probably get some testing done in hopes of uncovering any problems there might be.)
I hope you get things straightened out and are able to exercise without symptoms!