I know this thread was from a few years ago but OP did you ever figure out what was wrong? Similar issue with my 4.5yo of always saying their stomach hurts but eating/pooping fine and no other symptoms. About two weeks now. Already been to the pediatrician once where they checked her over and tested for UTI (negative). Put another call in and waiting to hear back.

When she originally started complaining I thought it was anxiety about something at preschool but the complaint has continued even after over a week at home.

Please make sure you are practicing food safety. Cooking everything to the appropriate temperature, not letting leftovers sit out too long, not cooking expired food, etc. I spent my whole childhood with nondescript stomach aches and pains and it all quit when I moved out of the house. When I go back to my parents' house now as an adult I can't believe their food practices. Leftovers on the counter for 2 hours, re-refrigerated, brought back out the next day to sit for another 2 hours. Stuff cooked that is still cold in the middle, etc. Somehow their gut bacteria has either evolved to process this crap, they are used to constant stomach discomfort, or they are just incredibly lucky. But I'm surprised I didn't die of food poisoning as a kid.

Anyway, I'm ranting here, but basic summary is that it's quite possible to have an excess of bacteria in food that can cause stomach problems without manifesting in the full blown form of food poisoning that is recognizable as vomiting, fever, etc.