Accented Characters Show as Boxes

[Charles Fish]

I am attempting to use the MySQL Migration Toolkit to migrate from SQL Server 2000 to mySQL 5.0.

The SQL Server DB uses the default latin collation; however if I use the latin collation in the settings to migrate, certain tables do not migrate over correctly (they have no data in them). If I use the option to use utf-8 everything migrates fine, however when running queries on the data, all characters with accents and certain special characters show up as boxes in mySQL's tables.

I have done some collation tweaking but that has not helped.

Any ideas what should be done? I could be overlooking something.

Thanks

Charles