If you are having problems with using PHP5 and MySQL on the same Windows system, I have the solution. When I upgraded from PHP4 to PHP5 I had kept the MySQL the same. The MySQL databases worked with PHP4 but they did not work with PHP5. After I installed PHP5 I saw that I could not connect to the database.
In order to fix the PHP5 MySQL issue you have to copy the libmySQL.dll file from php/dlls to c:\windows\system32 and you have to change this in the php.ini file:
"extension_dir = c:\php\extensions"
make sure you uncomment this line:
extension=php_mysql.dll
After doing this, PHP5 and MySQL started working together nicely.