I was unable to reproduce this issue on my system.
A few follow-up questions:
Since SHARING and PREFERENCES appear on two different menus in a default version of FileMaker Pro, are you using some form of custom menus in your solutions?
Does it matter what file is opened first?
Does it happen if, for example, you create two files based on two starter solutions?
Any plug-ins being used in your install of FileMaker Pro 12?
This appears to be a custom menu issue or a corrupted custom menu issue. I am working with a 20 file set of JobPro 6 files ( and additions ). There is a Custom menu called FileMaker Pro Copy. The menu contained the two items that showed in the picture attached to the original post.
I created a copy of the menu and removed the two items. They don't appear to be required, since the Preferences item is there with or without the custom menu and the sharing menu item is on the File Menu.
Once I updated the Custom menus in all of the files in the set, the issue resolved.
This may still be a bug. You should try and create the sub menu items and see what happens
FileMaker 9,10,11 Certified Developer