I am on the VPS atmosphere and so i have root access, btw.

So have a look at these problems: http://www.sonikastudios.com/wp-content/themes/sonikas/scripts/timthumb.php?src=/wp-content/uploads/tedleescreenshot1.jpg&w=100&h=100&zc=1&q=100

That returns a 404 error.

However, if I move timthumb.php towards the cause of the website, it really works.

I verified file/folder permissions, it isn't the problem. Also, another PHP produced image which i use for Captcha, does exactly the same factor...

So basically it boils lower to numberperl files running from inside folders. This really is no problem otherwise because PHP scripts I've under /admin/ on other sites work fine.

So... what might cause this? Most forum articles I just read lean towards a mod_security problem, however i don't know how to start, as I am no apache expert.

Same error can happen once the file it self can also be writable. Make certain the file is 644 and never 666 !

This can be a trouble with your .htaccess file produced by WordPress. It redirects all demands for the site that are not wordpress-admin/ or perhaps in your uploads directory towards the index.php apply for WordPress (the request handler that queries for posts, etc.)

As you've root access, try searching for what's happening in Apache logs. To follow along with latest request you should use tail.

Which version of Apache you're running? During my configuration of Apache 2.2 you are able to follow error sign in terminal by invoking:

tail -f /var/log/httpd/error_log

It seems that default configuration of Apache 2.2 has error sign in /usr/local/apache2/logs/error_log, so my configuration isn't default.

If you don't be successful with error log, try also searching for information in access log, default location at /usr/local/apache2/logs/access_log.

Wordpress is most likely with a couple mod_rewrite rules to transmit every request to the index.php. There it’s examining the request and coming back a 404 status code if a person of their internals was asked for.