This has to do with sessions and login shells, versus normal shells.
When you start a new session (this is what happens when you log in, either via the virtual terminals or when you start a new desktop session), the login process creates a bare environment, and then your
tcsh will be invoked as a login shell and do its startup routine, which includes processing global startup files (like
/etc/csh.cshrc) and your
So in that case, you're sure to see all your changes.
When you start a "normal" shell (from your desktop environment, or by running
tcsh from an existing shell), the environment is not cleaned up and the global files are not processed (but your local profile files are processed).
Since the environment is not cleaned up, your new, normal shell inherits it from its parent (one of your desktop system's processes). That process had read the previous version of your profile files, so it still has the old environment variables set.
You'll see that your changes worked by logging off of your desktop session and logging back in.
tcsh man page for exactly what files are processed when.