I have try all solutions for your problem, and I have no more others solutions because I not understand the origin of the problem.
The only solution, if your want a dock of Emmabuntüs, it is the reinstall on a other hard disk, and you can found a other disk and make the test.
To run dock setup of Emmabuntus is this command : /usr/bin/start_cairo_dock.sh
but the problem it is not to run this command it is why the orignal dock of Emmabuntus was disappear and why you can arrive to install in you home directory. For reinstall the dock of Emmabuntus I have send you the command, see in your bow email, because I not have this message.