One thing I do know about comprehension is that each year his %ile goes down.
This happened with my son. I was totally confused because I knew that his comprehension was excellent and that his reading level was improving (a lot) year to year. I finally discovered that he wasn't actually reading the passages on the reading comprehension tests. We were homeschooling and I gave him a standardized test every year at home. The next year I made him read the passages, questions, and answers aloud. His percentile rank jumped back into the upper 90s (the tests were three grades above his age-grade). He was the same age as your son is now when this happened.
Anyway, it sounds like there is probably more going on with your son than that, but I thought I'd mention it anyway.
