How make patch in PHPStorm suitable for Drupal.org?
PHPStorm patching issues have a long history. I have corresponded with their staff more than once, about a year ago. They told me then, that my issue was taken up to developers, but never actually corrected it. Right now, PHPStorm issues patches incompatible with Drupal.org, and we can do nothing about it.

To create a working legit patch, you need git, and create a patch like this: git diff > patch_name.patch 

See http://drupal.org/node/707484

A number of PHP Storm request related to this issue have been merged into a single issue http://youtrack.jetbrains.com/issue/IDEA-92793