Hi Pavel,
Could you attach the output from phpinfo() as an attachment here (or, if you're worried there might be sensitive information there, you can email it to me directly at dion at wordpress dot org) so I can check to see what the paths PHP is seeing?
(to get the phpinfo() output, simply create a file called 'phpinfo.php' which contains the following: <?php phpinfo(); and put that into your WordPress folder that you're having the problem with, and load http://sub.something.com/phpinfo.php in your browser. After you've saved the page, or copied it to an email, you can delete the file )
Next, When you connect via FTP to the server, what directory do you see? I assume you see the www directory, and nothing higher than that?
Finally, You should be able to work around this temporarily (by that, I mean, until the bug is fixed) by adding this define to your wp-config.php file:
define( 'FTP_BASE', '/www/something.com/sub.something.com/' );
There is also FTP_CONTENT_DIR and FTP_PLUGIN_DIR available, but hopefully the single BASE constant should work.