Hi Doug,
Make sure you have at least 4022 update.
Under the list of mprovements:
http://www.graphisoft.com/downloads/archicad/updates/AC21/ImprovementsList.html#4022
“229252 EDIT/FAVORITE: Applying a Door/Window Favorite did not apply its Sill Height.”
Therefore, when applying your Favourites, check which is the default Element Transfer Set beng used - next to apply, click the arrow, open the menu, then choose Element Transfer Settings. Select the set with the favourite icon to the right, and check the settings under Window/Door to see if the Sill Height is checked.
James.
James Badcock
Graphisoft Senior Product Manager