Your stomach is a large muscle, which needs a lot of blood to function.
Either, as has been said, you are getting hypoglycemic (the knock or bonk), which means that your stomach hasn't the energy to digest food, so rejects it. You will feel bad if that is the case. Your legs will be burning. I've almost blacked out from it on a few occasions. I did once, but free beer (alcohol also lowers blood sugar levels) after a 400km ride through Dartmoor, Exmoor and Bodmin Moor was another factor in that case.
Or, when you eat, your stomach becomes full and is demanding blood to function. But when you ride up a hill, your legs demand the blood. You only have so much and your heart has a limit as to how fast it can pump the blood around your body. The legs are probably being favoured, which means that your stomach can't cope any longer with the demands of digesting food.
Either way, the best thing seems to be the old addage, to eat little and often.
You won't have a fast fat metabolism from riding less than 50 miles at a time, occasionally. More like 50 miles every day, minimum, would give you a good fat metabolism.
Also, your stomach will become more efficient at digesting food if you keep using it. When you exercise, your whole body function speeds up. Digestive system included.