This might solve it, check here:
(Updated: https://www.blender.org/manual/advanced/scripting/security.html 10.23.16)
Relevant text as follows:
In the File tab of the User Preferences, there is the toggle Auto Run Python Scripts.
This means the Trusted Source option in the File Browser will be enabled by default, and scripts can run when blend-files are loaded without using the File Browser.
Once enabled you have the option to exclude certain directories, a typical configuration would be to trust all paths except for the download directory.