One more thing is that before, when I hit links.domain.com I got ransfered to links.domain.com/directory which does not happen now

When you don't request a file name in a URL, Apache web server looks for an index file to serve, it finds index.php, which is included with the script, and that redirects the browser to the actual script. /directory/

If you see a blank page then try a different syntax in the .htaccess file.

If the problem continue, please let me know what version of Apache your server runs, and whether it is a Windows or Linux based server.

Well when I hit the link like this : links. domain . com I get a blak page BUT when i hit links . domain . com / index . php then I get redirected to links . domain . com / directory and the message is this one :

Not Found
The requested URL /directory/ was not found on this server.

Additionally, a 500 Internal Server Error error was encountered while trying to use an ErrorDocument to handle the request.

And the server runs on Linux Apache/1.3.41

Yes, and that is addressed in this FAQ entry..
http://www.dew-code.com/content/view/14/25/

The file named "directory" is the actual script, it just lacks the .php file extension

The included .htaccess (not the one in /admin) tells your web server to treat the "directory" file as a PHP script.

Depending on your version of Apache and how it is configured, the syntax in the .htaccess file will be different

For my server it's

ForceType application/x-httpd-php

for yours it might be

SetHandler application/x-httpd-php

You can try each variation by un-commenting one directive at a time in the .htaccess file and refreshing your web browser.

The FAQ link above also has other options that might work for you.

Do you have an example of how the .htaccess file looks like?

I mean mine has a lot of information in there ... and Im not sure if all that is needed!!!

Should this stand alone in the file?

<Files directory>
ForceType application/x-httpd-php
#SetHandler application/x-httpd-php
#SetHandler application/x-httpd-php5
#ForceType x-httpd-php
</Files>

The other info you see is optional, all that is required is the portion you have listed

<Files directory>
ForceType application/x-httpd-php
#SetHandler application/x-httpd-php
#SetHandler application/x-httpd-php5
#ForceType x-httpd-php
</Files>


Lines that begin with # are commented and ignored by your server, so if
ForceType application/x-httpd-php isnt the right directive for your server, try the next by toggling the comment

<Files directory>
#ForceType application/x-httpd-php
SetHandler application/x-httpd-php
#SetHandler application/x-httpd-php5
#ForceType x-httpd-php
</Files>

Still not working ?, try the next one


<Files directory>
#ForceType application/x-httpd-php
#SetHandler application/x-httpd-php
SetHandler application/x-httpd-php5
#ForceType x-httpd-php
</Files>

Some servers may take a minute to check for changes in the .htaccess file, so it is probably best to make an edit to the .htaccess file, save it, refresh the page, wait another 30-40 seconds refresh again. If it still doesn't work, try the next directive by toggling the commented line, as shown in the examples above.

Once you see the script actually running, you might want to look into the mod rewrite rules further down in the .htaccess, but they are only optional. This FAQ entry talks more about that, and why you might want to enable them..
http://www.dew-code.com/content/view/34/25/