Not the Template ... tried with beez
Not the forum update .... updated the forum on my site don't have that problem
Noticed some of the icons in your Admin menus are missing ... possibly consider checking the database ? (perhaps something previously installed/uninstalled has altered something ?)
Extension manager >>> Update ... Purge then search for updates
I backed up the site ... installed 2.5.6 .... played with and saved different settings
Your Home menu item is an Alias of your default Home menu item in main menu
Saved the default menu item as copy and that shows in page source
<meta name="robots" content="index, follow" />
Created a featured article menu item (Home 3) with same settings and that in page source was not showing a setting for robots meta.
(This is correct as index,follow is default and not normally stated)
Conclusion ... A database field for the default menu item got filled with the wrong data and editing the menu item does not change the data in the field
... Copying the default menu item allows the field to be filled with it's default data(in this case index/follow)
... Creating a new menu item does not place data in that field because it is not needed unless it is changed from default.