One of the phenomena that occurs on norm-referenced testing is that, near the top of the range of the test, the spread becomes less reliable. Her report that the test was more challenging supports this, as the existence of higher-level problems indicates a greater likelihood of capturing her full instructional range. On the 2-5 version, all the high performing students in the grade 5 norms were bunched up, because there weren't enough hard problems, so that it was difficult to precisely distinguish between, say, a 79th %ile performer and a 97th %ile performer. The reliability of a 95th %ile score at the top of the MAP 2-5 is much less than the reliability in the middle percentiles, because it is so close to the ceiling of the test that minor differences in raw score (say one or two raw score points), which may occur for reasons other than "true" skill levels, can skew the %ile quite a bit one way or the other. Now she's testing nearer the bottom of the item pool for grade 6+, with plenty of headroom above her. Consequently, the likelihood of a noticeable change in %iles between the 2-5 and the 6+ is fairly great.
Another factor is the adaptive testing system, which starts everyone from the same place when testing for the first time (roughly one grade level below nominal grade placement), and gives them a limited number of items to work up (or down) to their true level. It is possible that a high functioning student might run out of the number of problems administered before the system reaches her instructional level. If that is the case, you might see a bump in her percentile, at the winter MAP.
In addition, regression to the mean would predict greater drops in percentile on re-test for the upper extremes than for percentiles closer to the 50th %ile.
In the big picture, 95th to 89th is a noticeable, but not necessarily dramatic, drop in performance. It's only about half an SD, some of which can be explained purely by standard error of measurement. High scores usually have higher SEMs, according to the publisher's documentation.
Whether she will continue to be eligible for the program depends, of course, on your local district criteria.