DaveDog,
Last fall my daughter, 17 at the time, and I went through OW certification together. She had a heck of a time equalizing. In her case, not necessarily your son's issue, she was being very impatient. Like many teenagers, she has a problem with patience! I had to work very hard to help her learn to relax and give it time. We (the instructor and I) we finally able to get her down to 20' during our OW dives. She just had to be patient and go slow. She was trying too hard blowing against her nose and she wasn't giving her sinuses enough time to clear. Also, being unsteady in the water, she was doing alot of what I will call bobbing. She was moving up and down about 1-2 feet in the water while descending instead of moving gradually. I'd imagine that didn't help.
Anyway, we finally got her through it, but it wasn't very pleasant for her. She had a pretty bad headache most of the day, but she recovered quickly and had no ill effects. I think she just had unrealistic expectations about how tough it was going to be to learn and to be patient.