I have problems of burning pain.
In my case I got a Bartonella lesion in my stomach which acted like an ulcer. I have to take a medication for ulcers that coats my stomach. Even after it should have healed, I continue taking the medication to avoid the pain. I also take Zantac, but I have taken that before Lyme.
I have had a lot of stomach pain. I have both Lyme and Bartonella (Babesia, too), and the article by Virginia Sherr, a Lyme aware GI doc, explained my abdominal symptoms very well. She calls it "Bell's Palsy of the gut." When Lyme causes partial paralysis of the digestive system, all kinds of problems appear. The stomach can't control the amount of acid it produces, so you can alternate between too much (burning) and too little (poor digestion, cramping).
It is important to know whether you're having excess acid or too little, as taking antacids will help with too much, but make it worse if you have too little. I figured out that when I had heartburn, I had too much. When I had an ache and it felt like my last meal sat in my stomach for hours, I had too little.
It turned out that I also had high levels of h.pylori and campylobacter. A Prevpac took care of that. I also took a med called Xifaxin (for e.coli and parasites) and it helped too.
Sorry for the long winded answer. In my case, the answer was complex. But it could be as simple for you as a side effect of a medication. Many of them cause stomach problems if taken without sufficient food. (For me, Rifampin caused me additional stomach pain and heartburn, even when I took it with food. I switched meds when we figured that out.)
Does your stomach distress occur after a dose of meds or does it seem random?