Hey Joe,
I've just implemented it so that by default it will hide the alternate divs if they have no modules in them. However its possible that this change will cause a problem for some existing custom skins, so I've made it possible to disable it by setting HideEmptyAlt1="false" and HideEmptyAlt2="false" on the <portal:StyleSheetCombiner in layout.master to override this new default behavior.
This change is in the source code repository now.
Best,
Joe