I have a 7 year old with Aspergers who scores pretty high overall in reading. For example on the WJ iii Achv. test his broad reading is a 139. But his Passage comprehension was a 112 and Writing samples a 116.
A poster here was able to explain and validate how this can be common occurance with kids on the spectrum.

His Broad math -160 and written language- 145 are DYS levels,but my sons overall higher level language skills are only upper Average/High average. My sons reading fluency is very high though.

An achievement test of some sort would be very helpful for you to get a better understanding of his comprehension.