The "difference" is the difference between the two scores, the base rate is the percentage of the norming sample that showed the same discrepancy. Uncommon discrepancies (those that occur in less than 10% of the norming sample) are more likely to be significant.
IIRC, his low scores were primarily on measures of fluency, both in mathematics and in oral expression and written and oral fluency. This could be indicative of any combination of the following; an LD, poor fine motor and/or oral motor output, problems with attention, or problems with the fact that the material tested may have been so far below his working level that he had difficulty paying attention or generating appropriately complex responses. If the fluency scores were in the average range and only "low" relative to the very high achievement in other areas, that may be indicative of nothing more than age-appropriate motor and memory skills, which are, from a developmental perspective, to be expected even in highly gifted children.
Further investigation is warranted to determine which of these is responsible for this pattern, because that will determine whether any further intervention beyond the clearly needed academic acceleration is warranted. If there are LD, motor, working memory, or attention issues, they may not have shown up as issues in the classroom yet, because the work has been so far below his challenge level, but, if present, they have the potential to become bottlenecks as the pace and volume of written work increases, so identifying and remediating now would be preferable to waiting to see if he starts to struggle.
It is worth noting that fluency measures that fall within the average range are generally nothing to be concerned over: fluency measures things like speed and accuracy of written and oral output, and ceiling effects may come into play in these sorts of measures very early on. Very high scores in other areas can still create a "significant difference" between those measures and fluency, but that difference may be significant because it shows that higher-order skills are significantly advanced, not that fluency is lacking.
In no event should evaluating him for potential problems take precedence over appropriate acceleration now.
