gnome-terminal:keyboard shortcut launches terminal with / directory default!

When you type Ctrl-Alt-T, or whatever key combination you set for "Open a terminal window" in Keyboard Shortcuts, gnome runs a specific command. This is defined by the gconf setting /desktop/gnome/applications/terminal/exec.

Run the gconf editor from Applications > System Tools > Configuration Editor and have a look at the value of this key. You'll probably find that instead of being just "gnome-terminal" it has extra arguments such as --working-directory=.... Reset it back to just "gnome-terminal" and it should start up in your home directory.

If it doesn't, then your default profile may have something unusual set in its preferences. In Terminal, select Edit > Profile Preferences and go to the Title and Command tab. Clear the boxes for "Run command as a login shell" and "Run a custom command instead of my shell".

Note that the /desktop/gnome/applications/terminal/exec_arg gconf key is for when you ask gnome to run a command in a terminal. You shouldn't need to change this.

Most of your options are covered here.

Also, since you cleaned your gconf files, I took a look at mine. Seems like there are lots of references to various profiles. You might want to set up different profiles and see what happens.

Something weird.

If you set "Ctrl+Alt+T" then working directory is ~ If you set ie "Mod4+R" (mod4 is Windows key) then working directory is /