[eluser]Azafar[/eluser]
@hcabbos i can help you to fix your problem cause i have been set the codeigniter's environment on windows, linux and ubantu as well. But i am not understanding what is ur actual problem. Let me tell you the way how we set the environment in windows with and without htaccess.
Without htaccess
Step1: Place your CI files in your subdirectory
Step2: Modify Config file and change the base_url according to your sub directory eg
$config['base_url'] = "http://domain.com/test/";
This is the only change in your config file
With htaccess
Step1: Enable mode_rewrite.so from your httpd.conf
Step2: Place all of your ci files in your sub directory
Step3: Open config file and do the following changes
$config['base_url'] = "http://domain.com/test/";
$config['index_page'] = "";
save it and close the config file
Step4: Place the .htaccess file and enjoy codeigniter

Note: Don't forget to mention sub directory name in your htaccess. And if you are using CI without htaccess $config['index_page'] should not be empty.
These are some steps to set CI environment on windows. Hope it will work for you. Sorry if i missed anything.
Regards...........