I too was diagnosed with reflux. Apparently the reflux can make you have some trouble breathing sometimes, particularly if you cough a lot and therefore inflammation will occur , etc. I also hav discovered that thinkinh about breathing and breathing too deeply can make you feel like you can't breathe! I recommend doing yoga or yogic breathing if you feel this coming on.
If it doesn't improve the doc may recommend a chest xray which would rule out any issues. I also recommend to stop smoking.
I'm not a doctor, just have experienced this stuff. :)