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.
 
Do you use debug bookmarklets? 'Break at the first line' option could be also controlled via 'xdebug Break On' and 'xdebug Break Off' bookmarklets.
Check the "Force break at the first line..." in the PHP->Debug section of preferences.
BESIDES THAT, also check this setting:
The above didn't work for me because as far as I can tell if you're using Xdebug the only debug bookmarklets you get is start/stop and debug this page. I don't see any bookmarklet specific to stopping on first line, and neither the start/stop bookmarklets nor stopping PHPStorm from listening within PHPStorm fixed the problem for me.
To get it to stop I did this (on OS X):