Hi,
You only uploaded the dlls right?
You need to copy the contents of the /Setup folder from the MySql package into the /Setup folder of your site then visit the setup page again. In the past we included the MySql scripts in the main package, but we no longer do this to reduce the size of the main package, so now you have to upload the dlls and the /Setup folder to get the upgrade scripts.
Hope it helps,
Joe