How does he do reading nonsense words? If you google nonsense words you can pull up some examples or maybe a sample assessment. Examples of nonsense words would be words like "bim" or "lat"...you need to know/comprehend phonics in order to read the words, you can't read them from memory. If he has problems reading those kinds of words fluently, there is probably a reading disorder. I don't think being underchallenged would cause the issues you are talking about.
One of my old-coworker's daughters had dyslexia and it was not diagnosed until she was in high school. Since she had such a high IQ, she was able to use plenty of compensatory strategies and appeared average in reading even though she was struggling.
