The article is trying to make you think it's fishy by breathlessly pointing out he was notified two weeks after the end of the case.
The truth is Navy selection boards for both staff and line officers meet at the same time every year. He was in competition with all of the eligible JAG O-4s for promotion. There was no "special board" just for him.
JAG is a very competitive program. It's not necessarily fishy that he was passed over for promotion. One must wonder, however, how many O-4's that were promoted had argued before the Supreme Court, let alone won.