Increasing a timeout should only be applied when you have good reasons (complex data, remote connection etc.), but most scenarios are analyzed quickly.
Potential Solution for your problem: You are not providing a code standard as a parameter, so make sure that PHPStorm is calling phpcs with a proper coding standard, thus leaving out the
--standard parameter may cause problems.
In PHPStorm under Settings->Editor->Inspections, expand PHP and go to PHP Code Sniffer validation. There you should find a dropdown select labeled "Coding standard".
I wouldn't recommend using the default MySource as a value if you haven't got a good reason, instead select PSR2, for example.
The following command would be issued by PHPStorm, in this case:
phpcs.bat index.php --standard=PSR2 --encoding=utf-8 --report=xml