Try to reset root password according this topic:
http://dev.mysql.com/doc/refman/5.0/en/resetting-permissions.html#resetting-permissions-windows
It worked fine for me:
C:\MySQL\bin>mysqld-nt --init-file=C:\mysql\set_root.ini
C:\MySQL\bin>mysql -u root -p
Enter password: *****
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 3
Server version: 5.0.45-community-nt MySQL Community Edition (GPL)
Type 'help;' or '\h' for help. Type '\c' to clear the buffer.
mysql>
B.1.4.1.1. Resetting the Root Password on Windows Systems
The procedure for resetting the MySQL root account's password on Windows is as follows:
Log on to your system as Administrator.
Stop the MySQL server if it is running. For a server that is running as a Windows service, go to the Services manager:
Start Menu -> Control Panel -> Administrative Tools -> Services
Then find the MySQL service in the list, and stop it.
If your server is not running as a service, you may need to use the Task Manager to force it to stop.
Create a text file and place the following command within it on a single line:
SET PASSWORD FOR 'root'@'localhost' = PASSWORD('MyNewPassword');
Save the file with any name. For this example the file will be C:\mysql-init.txt.
Open a console window to get to the DOS command prompt:
Start Menu -> Run -> cmd
We are assuming that you installed MySQL to C:\mysql. If you installed MySQL to another location, adjust the following commands accordingly.
At the DOS command prompt, execute this command:
C:\> C:\mysql\bin\mysqld-nt --init-file=C:\mysql-init.txt
The contents of the file named by the --init-file option are executed at server startup, changing the root password. After the server has started successfully, you should delete C:\mysql-init.txt.
If you install MySQL using the MySQL Installation Wizard, you may need to specify a --defaults-file option:
C:\> "C:\Program Files\MySQL\MySQL Server 5.0\bin\mysqld-nt.exe"
--defaults-file="C:\Program Files\MySQL\MySQL Server 5.0\my.ini"
--init-file=C:\mysql-init.txt
The appropriate --defaults-file setting can be found using the Services Manager:
Start Menu -> Control Panel -> Administrative Tools -> Services
Find the MySQL service in the list, right-click on it, and choose the Properties option. The Path to executable field contains the --defaults-file setting.
Stop the MySQL server, then restart it in normal mode again. If you run the server as a service, start it from the Windows Services window. If you start the server manually, use whatever command you normally use.
You should be able to connect using the new password