I\'m having this weird problem. All my settings used to work OK, until I updated my version of PHP. I use macports and have the php5 and php5-xdebug ports installed.
My problem with PHPStorm was that I was doing Drupal and the index.php was outside the project (since the project is a module). I needed to uncheck the settings "Force break at the first line..." in the PHP->Debug section of preferences.