It's been a while since I've used the Migration ToolKit...but isn't there an option to use an existing ODBC connection? Or do you need the jdbc driver? Does it give you an error message or a stack trace?
Have you tried checking the
mysql forums? Also, I'm pretty sure there are a few issues if you're migrating from Access or Oracle that are discussed in the toolkit help documentation. Maybe there's something tricky with MS SQL too?