I know you've had many responses and I admit I have not read through them all.
I was born with LGH which is Low Growth Hormone, typically found in dwarves. I was 5lbs and 18.25 inches when I was born at 41 weeks. I was never on the curve as a child... in fact, I had my own chart. My ped did not compare me to other children - she compared my growth against my previous measurements to make sure I was growing, even though it was at a slow rate. I was a little over two feet tall and weighed around 22lbs when I started kindergarten. Over the years, I was always significantly smaller than my classmates.
However, though as an adult I am still small statured at a petite 5'0", but I am over an inch taller than my sister who was born with normal levels of growth hormone and who was 5.5lbs and 19.5 inches at birth. I was tiny until I hit puberty, which came late because of the low growth hormone. Our parents were not overly petite - mom is about 5'2-5'3 and dad was about 5'9-5'10.
My own son, who is now eight, was born at 9lbs and 21.25inches long. he is now the smallest kid in his class (go figure). He's shorter than most of his classmates and also very thin. His father is 5'11 and was the same way as a kid... very lanky.
If the tests rule out things like issues with gluten, thyroid diseases, and growth hormone anomalties, and your son is consistently growing (even at a slow rate), then I wouldn't worry about it too much right now. If he is otherwise healthy and thriving, and meeting his milestones, then he may just be small statured.
Also, make sure he is getting a balanced diet - proteins, fruits, vegetables, etc. At this age, he should be eating mostly solid foods, so make sure he is getting enough. Especially since the daycare he was at wasnt feeding him.
I hope you reported them.... they should not be in business.
If you still know in your heart something isn't right and you arent getting answers from your current doc, get a new doctor for your son.