I am so sorry for your family's trials. Especially sorry to hear about your six year old nephew. Here are some ideas about brain lesions in epilepsy from another board- these would not be demyelinating lesions, which is probably why the docs say no to MS.
"Epileptic lesions are areas of the brain that are abnormal that allow synchronous discharges of brain activity that eventually induce seizures. These lesions can be a variety of things, neuronal migration abnormalities, atrial-venous malformations, tumors, strokes, infections, sites of hemorrhage, etc. They can also be genetic, such as a ion-channel abnormality. There are some that are due to immaturity of the brain. There are many more that we are only beginning to understand, but the point is that there are many, many things that can cause seizures."
Hope you get some answers really soon. Good thoughts to your family-