It's possible he did get off on the Scantron - I've had that happen with one of my kids and it made the difference between a typical score of 99th percentile to a 62nd percentile. However, I think it's really rare that this sort of thing happens, and my ds who had the issue has a diagnosed disability that impacts the ability to do things like fill out Scantron sheets soon... I wouldn't necessarily think that was the case with a nt kid. My gut feeling is that the difference in scores is reflective of strengths vs areas that aren't as strong for your ds. I'm not familiar with the NNAT so I can't help you with it, but hopefully aeh will stop in and help out with it (or you can also often google and get detailed info on what types of subtests are part of a test, how it is administered - group, individual, oral vs reading questions etc). Then look back at your ds' WISC report - if the GAI was used, that means there was a discrepancy in either working memory or processing speed subtests that made the FSIQ calculation not valid. There may be a clue in that info if you find a dip in either WM or PSI scores - it could suggest a relative weakness that might, in turn, have a larger influence on the NNAT (which I suspect is not as comprehensive of a test, therefore less subtests than the WISC, therefore a subtest that is weighted heavily on WM or PSI-type tasks might carry more wait in the full score).
I'd also look and see if there was any discrepancy between the VCI and PRI scores on the WISC - that also might correspond to a lower NNAT score.
Last thing - it's possible the WISC at a young age was an overestimate, and it's also possible that your ds simply wasn't performing up to his ability on the NNAT. The thing about tests is any one test all by itself without any other supporting data is just that - one piece of data. Have you looked into the requirements for admission to the public school's GATE program? The NNAT may be used as a screener to id kids who need to be tested further, but is it the only criteria for admission? If it's not - for instance, if it's given as a first-round screener and then other criteria are considered such as teacher recommendations, parent recommendations, other ability tests etc - then you can put together an appeal and advocate for placement.
Best wishes,
polarbear