This is a tricky one as basically there are 1001 reasons this could be happening.
First off have you been checked out by a doctor. There are conditions that can cause this & only a doc can really make sure you haven't got anything. I do doubt it is anything serious as it been going on your whole life & if it was well you'd be really sick by now, but we always have to suggest you get it checked out.
My first suggestion would be "well work out at night". It isn't really bad to eat at night if that's the time you can do it either, so eating & training at night seem like a good course to steer for now while you try & sort out how to deal with your condition.
It would be good to know what you have tried so we can get an idea & assuming it's not a medical condition we can try & figure out options from there.
Bear in mind this is one of those conditions that is basically try 'a' & see if it works, if not try 'b' etc as there are many reasons from allergies to unfriendly bacteria in the tummy, even things like the acidity of stomach acid might be a factor?
So, what have you tried & if you can remember results , also what are you doing right now & some idea of your diet & training would be nice.
Oh yea also bear in mind although I'm a fully qualified sports nutritionist, I'm only part-way through my nutritional consultancy course, so any advice has to be "If I were you then I'd do..." type of answer as technically I can't prescribe diets yet.
Also if anyone else has come across this before or has any ideas I'd be interested to hear how they would deal with it too.