A couple possible thoughts come to mind:

* what epoh said smile
* a non-verbal learning disability. If your math issues were related to a NVLD, that could be heritable. Does she have trouble with visual spatial reasoning (rotating things in space, for instance or recognizing how something would appear from a different angle)? Does she have any trouble in math?
* speed issues; the test is timed after grade two

Although my 2e HG kid did, by far, the best on the non-verbal section, I don't know that I'd say that part is the most tied to intelligence. Mine overall did a lot better on individually administered IQ tests than the CogAT and I'm, thus, not as huge of a fan of groups tests (well, that and that the test producers specifically say that they aren't meant to measure intelligence, but learned skills). I would say that the non-verbal section comes the closest to the types of things measured on part of IQ tests but really only the parts that look at perceptual or visual spatial skills. A child with high abilities in other areas who has that one weaker area may still be gifted or the test may just be a poor test for that child.