Mysql 5.0 on Windows 2008
There are three(3) aspects you need to consider
ASPECT #1
You may find this astonishing but did you know that some older versions of MySQL can outperform newer versions ? You must tune MySQL 5.5 properly. In fact, InnoDB has new options introduced into the InnoDB Plugin.
I have earlier articles in the StackExchange on this

Jul 16, 2012 : decreased performance of stored procedure when migrated from mysql server 5.0 to 5.5
Feb 22, 2012 : MySQL 5.1 vs MySQL 5.5 (5.1 twice as fast)
Nov 24, 2011 : Why mysql 5.5 slower than 5.1 (linux,using mysqlslap)
Jun 19, 2011 : How do I properly perform a MySQL bake-off?

ASPECT #2
Looking at the my.ini, something caught my attention: you have innodb_thread_concurrency=10. That's a definite no-no, especially with MySQL 5.5. I say this because MySQL 5.x thrives on setting the innodb_thread_concurrency to 0. At Percona Live NYC 2011, Ronald Bradford explicit told me as I sat in the audience not to set this to any other value than 0. By setting it to zero, it lets InnoDB figure out the correct number of threads it needs create.
ASPECT #3
You need to activate multiple cores for InnoDB. MySQL 5.0/5.1 are not designed to use multiple cores. The InnoDB Plugin (from MySQL 5.1.38 has new options for doing so. Those options are fully present in MySQL 5.5. Such include

innodb_read_io_threads
innodb_write_io_threads
innodb_io_capacity