Wow! I can sense that you are seriously worried. That in itself will make your son feel that something is wrong; perhaps he's not good enough, etc. He can sense your tension even when you think that you've hidden it.
I wonder why you don't trust his doctor. I'd recommend getting a second opinion so that you can stop worrying.
If your son is meeting developmental goals I feel strongly that he is OK. I've seen many failure to thrive babies and that description does not fit what you have told me about your son. Failure to thrive is a medical term meaning that the baby weighs near the bottom or even off the chart. Your's is at the 50th percentile. That's good. Failure to thrive also means that the baby is not learning at an average pace when combined with being extremely low in weight. Have you looked at the developmental charts? Since his doctor says that he's Ok I think that he is maturing as he should.
Your baby is in the 90th percentile in height. The only thing this means is that he is tall and when his weight is in the 50th percentile he'll be thin. These numbers describe a healthy kid weight wise.
Next visit the numbers may be different. My grandson was in the 97th percentile for height and the 90th for weight when he was born. At his 6 month visit the numbers were further apart. At his vist when he was 27 months old the numbers were nearly as far apart as your son's. Something like 90/40. He was and is healthy although he was and still is thin.
My granddaughter grew the same way. She's still thin, a "long drink of water" or "skinny as a bean pole" as my parent's would say. The babies in our family have mostly been plump until they started walking. Then they gradually grew thinner. A cousin had a baby that was thin since birth. The aunts would speculate on whether or not she was getting enough to eat. As they saw that she did all the things that babies are expected to do they relaxed. This cousin's baby is still thin as an adult but like the rest of us tends to put on weight as she ages.
Thin babies have an advantage over us plump ones. They are less likely to be obese as children and adults. We're seeing the newest generation have a high percentage of obese children. This is not healthy.
My uncle was tall and thin all of his life. Yet he was healthy. Tall and thin is OK. In fact we are deemed healthier if we stay on the slim side as we grow and then age.
The percentile chart is based on the weight and height of many children. It's a mathematical chart and in itself tells you very little about your child's health. Your son's numbers only mean that 50% of the kids who are weighed weigh less than he does and 50% weigh less; 90% of the kids are shorter than him and 10% taller. The chart is only used as a comparison. Frequently kids' percentiles are as widely spaced as your son's. Babies and children grow up and then out. Or perhaps out and then up. They do not do both at the same time. 50/90 is a good measurement.
A another child may be in the 50th percentile for height and 30th percentile for weight. This is still OK. The numbers by themselves have little meaning. They do have meaning if the numbers over time change their pattern. The doctor is also checking how he is developing in other ways. He combines all the information that he gathers to determine if a baby is healthy.
There have been numerous studies done that show that babies will eat what they need when they need it. I remember one during which food was put out for toddlers. Frequently they would chose to eat the same food for days before they switched to another food. Their diet was balanced as they chose their food. We are born with an inate ability to know what our body needs. We lose that ability as we become socialized.
We also are able to sense our parents feelings much better than we do adults. A baby "knows" that he is totally dependent on his parents. If they don't take care of him he will die. He lets us know what he needs by crying. Another study determined that babies cry differently to express different needs.
So trust your son's ability to eat what he needs. It's your role to provide the food for him. From what you've said you do provide him with healthy food. His height and weight are healthy heights and weights. His pediatrician says he's healthy. If you can verbalize why you're so concerned perhaps his doctor will be able to run further tests, tho I can't think what they would be.
My grandchildren have always had times when they ate really well while at other times they hardly eat anything. I frequently feed them dinner and I've noticed that my grandson, who is now 4, tall and thin, is eating very little at dinner time. Even when we have McDonald's Kids meal which he's always eaten well until the last 2-3 weeks. My mother would say he's reached a plateau in growth; therefore doesn't need as many calories as he does when he's growing. This pattern is usual and healthy.
So, if you're still worried talk with the pediatrician. If you don't trust him see a different one. But beware of becoming one who shops for doctors until they find one who will agree with you.
Relax and enjoy your son. Before you know it he'll be taller than you and if he's lucky also thin. If you keep worrying about food he may develop problems with food and become skinny in an unhealthy way or fat in an unhealthy way. Food is just one small part of our daily life. If we focus just on food, food becomes an emotional part of our life when it should just be what we eat every day. Some days more, some days less.
Here are 2 web sites that explain the use of growth charts as well as eating. These sites have articles that provide more information.
growth chart explaination
http://kidshealth.org/parent/growth/growth/growth/_charts...
about eating and power struggles
http://wwwbabycenter.com/o-how-to-avoid-making- meals-a-power-struggle-###-###-####.bc