I came across a short thread started by James Starlight last month (December) which was not resolved, and I have been having the same issue. I upgraded to v1.6 in December, and since then am unable to load the autodock plugin. When I go to import autodock.py, I get the following error:

Unable to initialize plugin 'autodock_plugin' (pmg_tk.startup.autodock_plugin).
 parser: matching files:
  autodock.py   autodock.pyc
PyMOL>import autodock.py
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 260, in parse
  File "<string>", line 1, in <module>
  File "autodock.py", line 48, in <module>
    from numpy import *
  File "/usr/share/pyshared/numpy/__init__.py", line 137, in <module>
    import add_newdocs
  File "/usr/share/pyshared/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
  File "/usr/share/pyshared/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
  File "/usr/share/pyshared/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
  File "/usr/share/pyshared/numpy/core/__init__.py", line 5, in <module>
    import multiarray
ImportError: No module named multiarray

After searching online, it sounds to me like this is a combination issue -- often with Debian users (which is what I am using) there are issues importing numpy. But when I execute python from the shell and import numpy, I get no errors:

blake@NEI-GPU:/tmp$ python
Python 2.7.6 (default, Jan 11 2014, 14:34:26) 
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy

So I don't know if there is also an issue with pymol. I would greatly appreciate any help from the community, because Daniel Seeliger's plugin is orders of magnitude better than autodocktools, and I don't want to contemplate going back to the dark ages of analyzing my docking results....