One thing to consider (and I have absolutely NO way to gauge if this is the case with your son, but it's something worth thinking about) is his learning style. Kinesthetic learners are often the math and science types, but unfortunately our schools are geared toward visual and auditory learners. If a child is not a visual learner, he may simply not try when it comes to reading, because it is almost entirely visual. My DS has a similar problem - he is tested as slightly above grade level in reading, but not much. At home, however, he reads my college textbooks - not completely understanding them, but enough to ask good questions. Because it relates to something that interests him, and he can apply what he reads to real life situations. I was actually told once that he had problems with visual processing - but farther testing showed no disability, just that it was not his strong point.
Is it possible this is similar to your son's situation?