I know this is an old thread, but I was just having this issue myself and trying to find out how to deal with it. What I think the originator of this thread was describing was the difference between how well Maplex seems to label contour lines with how poorly they appear after converting to annotation. I've attached two screenshots. The first (LabelsByMaplex.jpg) shows the generous placement of labels by Maplex (shown with a halo around the labels):
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Contrast this to the comparatively stingy placement once converted to annotation (LabelsAnnotation.jpg), shown using feature outline masks (a little harder to spot):
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I've not found anything else on this so far.