I've been building multi-language Joomla sites since J1.5 - most with more than 10 languages. In J3.x I'm finding that the ordering in the language selector seems to be broken. Here's how it's supposed to work (from the Description of the Language Selector module):
The way the flags or names of the languages are displayed is defined by the ordering in the Language Manager - Content Languages.
This holds true if I use the Dropdown menu - the order is the same as in Language Manager > Content Languages. But if I turn off the Dropdown menu and use either a horizontal or vertical image display the order goes crazy. It does not revert to ID order, native title, or any other order I can see.
I'm attaching screen caps showing a site in development with 15 languages - the drop down shows the correct order. The horizontal flags show the crazy order.
My work-around is to use the Dropdown menu but my clients like the look of the flags. Never had this issue with J1.x or J2.5 but it's the second J3 site I've built with this issue.