Hopefully you did not use the same db name as the file may still live on disk from the 5.1 installation.
Did you set your connection string to the new empty db?
Did you visit /Setup/Default.aspx again after creating a new db?
Did it run the scripts with no error?
What is the error now and what steps to produce the error?
This site is running on MySql on windows with no problems and my local machine it works with no problems.