It appears the default for the starting directory when using nautilus-open-terminal from the right click menu has changed. Previously when right clicking on the desktop and choosing ‘Open Terminal’ you were given a prompt in your home directory. With Fedora 9 when right clicking on the desktop and choosing ‘Open Terminal’ it now defaults to your Desktop directory. Now this does make sense as to why it does that – but it isn’t like it used to be!
It is easily changed back to the ‘old style’ though if you are so inclined. Make sure you have gconf-editor installed – if you don’t you can run yum install gconf-editor to install it. Then run gconf-editor and expand the ‘apps’ section and scroll down the list to ‘nautilus-open-terminal’. On the right hand side, place a check mark in the box for ‘desktop_opens_home_dir’. Close gconf-editor and now you are good to go!