It's a clear case of
indigestion in children called 'mandagni' in Ayurveda. As you have seen yourself that upper GI showed normal.
So the problem remains with functioning of digestive system and enzyme secret which is causing mushy stools etc.
My recommendation is that non toxic, natural herbal treatment should be given to your child.
BAEL fruits pulp (dried) plays an important role in such conditions. If you can get it - nice. Otherwise get online from South East Asian countries esp India. Himalaya herbal co. also has BAEL cap containing BAEL extract. It markets the same globally.
Now your small child would not take Capsule. So open/ cut the capsule and pour into a bowel. Mix honey and let the child lick it. Do it twice or thrice.
Alternatively if you get BAEL powder (also called Bilv powder) from India, give it at least 1/2 gm with honey twice or thrice a day.
After giving for a week or two you may add little (250 mg approx) dry ginger powder also once a day to BAEL powder and if child accepts its taste, continue it for a week more.
It will flare the natural enzyme secretions. It is
astringent, antimicrobial, antiinflammatory, antispasmodic etc without any toxicity or side effects.
BAEL is also called stone apple, wood apple.
For any other query pl write direct question.
Hope it is helpful.