I know my homegrown ones that are full of flavour are very acidic and give me hives. The commercially produced watery tasteless ones are lower in acid and give me no problem. I imagine acidy ones could give you problems. Why not try giving them up for a month then start again and see what happens?
I am not sure if you are aware but in most people it is not the acid in tomatoes which causes GI problems. There is an unknown chemcical in tomatoes which in some people triggers heart burn and other such symptoms. I assume your home grown ones cause you more problems then store bought is because homegrown is more fresh and has more nutrients.