I was having these problems with Windows and long file names etc however installing the latest npm fixed the issue because version 3 onwards I believe (and as Mike Hartington has also commented) creates a flat dependency tree structure for node modules.
Regardless if you have a recent version of Node, do this:
npm install -g npm
Note that npm is updated more frequently than Node, so the latest Node version may not necessarily have the latest npm version.
The latest npm version at the time of writing is 3.8.8.