We've seen wild fluctuations even in IQ scores with my dd9. Her CogAT scores also are above avg (about 1 SD or so), but extremely far below her IQ scores and she had totally different strengths and weaknesses btwn the two tests.
I think that the more important questions are:
Why did they retest her on the CogAT? Does it matter for anything in terms of school placement, etc.?
and
How is she doing with her current placement? If she is performing well in the GT classes, I'd assume that it is a good fit regardless of one score saying that she is not qualified. If you think that she needs more than the programming she is in (acceleration, etc.), then I'd look at doing above level testing for achievement to see what she knows.
I do believe that ability matters. Children who don't have gifted ability probably shouldn't be skipping grades for instance, but some children are just inconsistent on tests. I've been told by at least one GT professional that it is better to assume that the higher score is more accurate b/c you are less likely to guess well enough to test beyond your ability than you are to have a bad day and test lower than you are able.