Comment 4 for bug 128493

You asked for a simple step-by-step instruction how to reproduce.
What part of the original post needs more explanation?

Here is a more elaborate version:
1. if you are using a fresh install, start firefox and create a bookmark
2. from a terminal window: $ sudo nautilus (i.e. start nautilus as root user)
3. using the nautilus browser, find a .html file and open it with the mouse
(e.g. file: /usr/share/gtk-doc/html/evince/index.html)
(this starts firefox as root user)
4. firefox should start and display the html file
(if not, right click the file and in the "open with" dialog, select firefox)
5. exit firefox
6. open firefox again
7. check the bookmark created in step 1 - it is now gone

In fact, all user files in the firefox profile have now been replaced with initial versions.
The owner of these files is the user, not root.

If firefox is started as root user using $ sudo firefox, the problem does not occur.