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NWEA MAP is an achievement test designed mainly for progress monitoring. CogAT is an aptitude test used to predict learning ability, and is supposed to be less vulnerable to differences in instruction. Performance on achievement tests, especially in mathematics, is very much a function of access to high-level instruction. Even a very bright little person shouldn't be expected to have to independently re-derive high-level math principles in order to achieve in the top percentiles on material to which they have had no exposure.
So at the simplest level, it is possible that your child has not performed above a particular percentile just because of the range of topics in which he has received instruction. Some children also find the CogAT reasoning tasks more engaging (as they are like puzzles), while math problems may feel like drudgery, even if (especially if) they are easy, which can lead to careless errors.
Finally, once you reach the top few percentiles, the fineness of discrimination really isn't there. Even on an adaptive test, it's difficult to distinguish between 95th and 99th percentile in only 35 multiple choice items.
I would withhold judgement until the GT teacher completes her testing. It sounds like she is an advocate for him already, particularly in math (quantitative reasoning and nonverbal reasoning are probably the sections she has completed) so a small difference in the numbers is unlikely to change her attitude to him that easily.
