Comment 5 for bug 269109

To answer your question, the paths in the commands above are absolute, so they will work no matter your current working directory.

When you attempt to upload a new extension / module / template in the joomla administrative interface, are you getting an error?
If so, what is the error?

FYI - this bugfix has been incorporated in the latest TurnKey Joomla release (turnkey-joomla-2008.10.17-hardy-x86), aswell as other fixes/changes (http://www.turnkeylinux.org/appliances/joomla/releasenotes).