sully, was this score on a WISC IV or another test (I believe the WPPSI may have or also has a GAI)? This may be helpful from the Davidson database:

"What does it mean when a child scores within the gifted range on the Verbal Comprehension and Perceptual Reasoning Indices and shows much lower scores on the Working Memory and Processing Speed Indices of the WISC-IV?

It is common for gifted children to show significantly lower scores on the Processing Speed and Working Memory Indices of the WISC-IV, when compared to their performance on the Verbal Comprehension and Perceptual Reasoning Indices. However, very large discrepancies can sometimes be indicative of problems with attention or something else that is getting in the way of a child being able to focus or process and respond to information quickly (i.e., anxiety, depression, visuomotor coordination, perfectionism). When this is the case, a comprehensive neuropsychological evaluation would be required to help tease this apart.

What is the General Ability Index (GAI) of the WISC-IV?

The General Ability Index (GAI; WISC-IV Technical Report No. 4, 2005) provides an estimate of general cognitive ability that is less sensitive to the influence of working memory and processing speed. This may be used as a substitute for Full Scale IQ to determine eligibility for placement classification. The GAI is often used instead of the Full Scale when assessing gifted children. Because the processing speed index (PSI) and working memory index (WMI) of the WISC-IV are not the best indicators of intellectual ability, many clinicians don’t administer them when assessing for giftedness and it is not uncommon to only report the GAI .
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My understanding is that it is NOT uncommon for a HG+ child to have a higher GAI than FSIQ, and that it is not necessarily indicative of a learning disability.

I will defer to someone more knowledgeable about the rarity of the score, but I believe that most charts I have seen suggest that it is well above the 99.9 percentile.