The key to understanding tempdb is that at startup of SQL Server, it is created based on a "template" found in sys.master_files. This determines what your tempdb will look like at startup. Unfortunately, the SSMS GUI doesn't reflect the fact that tempdb is different from all other databases, hence it is confusing.
I've written a blog post about managing tempdb, hopefully sorting out the mess that this re-use of GUI causes. You'll find it here: http://sqlblog.karaszi.com/managing-tempdb/