Path problem with Drupal CVS

I yesterday replaced Drupal 4.1.0 with Drupal CVS and I have some path problem. When I define $base_url = "http://www.domain.com"; I can't log in or anything else. I get some limited functionality with defining base url as $base_url = "http://www.domain.com/index.php"; but I think there must be better answer.

OS: WIN 2000
Database: MySQL
Web server: IIS

Thank you very much.

Regards,
Gaba