Reasons for Many Large Cafe Au Lait Spots in Son Still Undiagnosed.

I hope the geneticist can help you. If the spots are what is called Cafe au Lait spots, this is most often caused by Neurofibromatosis. My husband has it, and my son has the spots. That's ALL they needed to diagnose it in my son. It is genetic, 50% chance of passing it on, but no one further back than my husband has it in his family. For my husband, no day-to-day symptoms, but benign tumors under the skin that grew large enough to have to be removed. For my son, no symptoms but more frequent testing of eyes, ears, etc. to make sure nothing's happening.
Forgot to add, my son has light skin, and the spots look like giant freckles or birthmarks.

Dark spots on children that have darker skin can sometimes be Mongolia Spots. But I am not sure anything else is in that diagnosis.

I certainly hope you find a doc that will take you guys and find out what is wrong. It sounds miserable.

People with McCune-Albright Syndrome sometimes have cafe au lait spots.

My son is nine and has several cafe au lait spots. He is half hispanic and these spots are more common in asian/african american and hispanic people. My son's ped sent us to a geneticist to rule out neurofibromatosis. They could not say 100% that he didn't have it, but were reasonable sure he didn't. We also had his eyes tested to help further rule out the possibility. We could have pushed for more genetic testing, but since my husband has several and is ok, I decided to drop it. I would push for the genetic testing just for peace of mind.

Have you thought about contacting Children's Hospital? They have all sorts of specialists that could help.