Laz,
Sorry that you are seeing this issue.
Can you please answer some more details to help us investigate further :
1) Can you please share the Installation Details from MyEclipse > Installation Summary > Installation Details ?
2) Can you please make sure whether you have selected Dialect as “org.hibernate.dialect.MYSQLDialect” and also selected Metadata Dialect as “(default)” .
3) Can you please try scaffolding for a single sample table in MYSQL by following this tutorial and let us know if you can replicate the issue ?
http://www.myeclipseide.com/documentation/quickstarts/scaffoldingtutorial/scaffolding.html