The bacteria the GI doctor was talking about, from acid reflux, is called Helicobacter Pylori, or "H. Pylori" for short. A very simple blood test can/will tell your doctor if you have it or not, and, yes, it CAN cause certain things, but, I don't think the doctor meant that you HAVE any tumors or polyps... the doctor will not know that, without doing a colonoscopy, and endoscopy.
Simple stomach problems, (well, not 'simple, they can cause horrible illness- I know this if anyone does!!!!) but, stomach problems... do not indicate HIV/AIDS.
I'm not sure how you are worrying about AIDS, due to stomach problems (acid reflux).. it sounds like you may be very 'fixated' on HIV/AIDS... it is good to be AWARE, and careful... but, don't let your mind take over..
If you tested already, every 3 months, for a year, and were negative, then, why so worried now, (and not having been sexually active????)
If AIDS is still a concern of yours, even after (4?) negative tests, mention this to your regular doctor, get tested again, so that you can stop worrying about it.
Take care