I noticed that Emacs was getting a default-directory value of / when launching it with a custom keyboard shortcut I set up in Gnome (2). The result is that opening a file started my search in the root (/) of the filesystem.

I suppose this is due to the way in which emacs was invoked (via the window manager). Given that there was no actual present working directory, I can understand that it would default back to using /.

At the time I was just setting the window title:

emacs -T Emacs

When considering how to work around this I first considered setting the default-directory in my .emacs file. This turned out to be a less an idea solution. Doing so causes it to become a global configuration value (all subsequent emacs launched via the terminal opened in ~). So instead, I changed my launcher command to this:

emacs -T Emacs -eval "(setq default-directory \"~/\")"

Works like a champ!