They display in alpha-numeric order when you restart MindManager, or at least they seem to for me. When I add a Map Part it gets added to the bottom of the list. Re-start and it then becomes sorted alphabetically
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Map Parts folders also sort themselves alphabetically when MindManager is restarted, except that the Favourites folder is always on top. It's interesting that the same doesn't apply to icon and tag groups on the Marker Index.