I agree. It is very odd the USAFA granted the waiver but not the USMA.
The USAFA has a large majority of personnel on flight status and a history of head injury is DQ for all flying classes. In other words, by the USAFA granting the waiver for your DS for a history of head injury, the service is already taking out a option (e.g. pilot, navigator, etc) for him if he were to go into the USAF. Granted, he'd probably get a waiver since it occurred when he was a child (my assumption).
The concerns for head injury are 1) relative risk of seizures and 2) residual neurocognitive defects. Studies have shown the relative risk of seizures for someone with a mild head injury (again, my assumption in your case because the waiver for the USAFA was granted) is higher for 5 years after the event compared to the general population. When did the event occur?
The other issue is residual cognitive defects. Another assumption, by the mere fact your DS has applied to the SAs tells me he has done well in HS and that suggests no cognitive issues.
It's hard to say which way the USNA will go since you got thumbs up from the USAFA but thumbs down for the USMA. My gut tells me it'll be close because from my experience the USN has generally been tougher with medical qualifications than the Army.