PphStorm 6.0.2 - Do you want the application to accept incoming network connections?

OSX 10.6.8 / PhpStorm 6.0.2 asks me "Do you want the application to accept incoming network connections?" every time it start the application, no matter if I accept or deny this dialog. It also asks me for keychain access when accessing git or svn repositories, answering "Always allow" does not help either.

What I've tried so far:

• re-downloding PhpStorm DMG, no change there
• removing PhpStorm from the OSX Firewall, interestingly on the first launch it does not ask, but on all following launches
• code sign it with my self-signed certificate, that worked on 5.x versions of PhpStorm, but now it fails
  sudo codesign -s "my codesign" -f /Applications/PhpStorm.app
  /Applications/PhpStorm.app: replacing existing signature
  codesign_allocate: for architecture x86_64 object: /Applications/PhpStorm.app/Contents/MacOS/phpstorm malformed object (unknown load command 8)
  /Applications/PhpStorm.app: object file format invalid or unsuitable

Thanks for any pointers.