I'm aware of a bug that prevents category menu items from being copied between two menus. If your site uses these types of menu items it will be a while until I can fix this problem since I have a daughter-to-be coming very soon.
In the interim, you could also install this plugin - http://wordpress.org/extend/plugins/duplicate-menu/ which although doesn't support syncing the hierarchies, does work with duplicating categories from what I've been told.
Another problem is that if you remove a page from your menu, my plugin won't update the structure for that page on sync. This is due to the fact that I allow syncing for partial menus - so if you have a specific menu for one part of your site that only contains a dozen or so items, I only intend to sync the pages listed in the menu to prevent undoing the rest of your site's page hierarchy. I can fix this programmatically by keeping track of menu items removed from a given menu between each sync, and remove them from the heirarchy if they match the menu structure before they were removed. But this too is a fix that will have to wait while I get used to life as a first-time father :D
I'll leave this ticket open until they're fixed in case anyone else notices these problems.