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There was evidently a problem with some horses whose scores indicated that they should have leveled up, but they hadn't. Another player posted about hers, and I checked and found that at least one of mine appeared to be in the same position, though not all of the ones I looked at were. This is one of the things Ammit mentioned she had dealt with in her post about recent work she had done. Perhaps your horses were among those affected.

http://www.huntandjump.com/forum/discussion/6919/fourm-update-and-some-other-stuff#Item_6

Lake Ondowa is correct as well. Leveled off horses do continue to gain very small fractions of a point with training, and if they were close enough to leveling up, they will do so when the score gets high enough.