[knc1]

A few of the things you should be doing:

*) First, update your PW-1 to the current, 5.6.1.1 firmware release (this thread is also the jb for that version).
*) Use the jail break attached to the first post of this thread.
*) Follow the directions in the first post of this thread.
*) Use something other than a MacOS, or disable the "safe archive" thingy.
That is, neither you nor your overly helpful MacOS should be opening any archive unless the directions specifically tell you to do so.

The resulting directory tree of opening an archive DOES NOT and SHOULD NOT include the name of the archive!
That is another matter of your option settings on your MacOS.

When directions here (written over a span of years, terminology changes) tell you to put something in the 'root' of the directory tree over USB cable - it means:
"Put in top visible level of the directory tree as seen over the USB cable, right alongside the /documents directory."

Kindle Linux is a single root directory tree, just like you MacOSx is and the top level visible over the USB cable IS NOT the 'root' of the directory tree.
It is a sub-directory of the system directory tree, exported for your use.