I think there are 'operational' areas of the wiat that show more what the child has learned, and 'comprehension' areas that show more what the child could learn/aka potential/ability. If the comprehension areas are high that might possibly put into question the wisc fsiq, which is supposed to be about ability.
Even if the higher score is mainly on operational stuff, that does indicate a good ability to learn...being in a good place to learn well helps. Do you have doubts about the fsiq? Is what your child doing day to day seem more than average?
I had this experience, though only lately did my ds take the wiat. The wisc did not particularly seem to show his real ability, but that is probably because is an odd fellow, running around the house taping everything to everything else...wears his creativity on his sleeve. Doesn't give the typical answers to typical questions, etc.