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FWIW, I noticed in the release notes for MySQL Connector 5.1.x, that some changes were made to the way schema metadata is reported. I remove the reference to 5.4.1.0 MySql.Data in the MyMeta solution, and added a reference to 5.0.7. After recompiling, I copied the new MyMeta.dll and the 5.0.7 version of MySql.Data.dll into the MyGeneration13 program folder.

FKs now show up under columns in MyMeta Browser. The template which loops through a table's FKs now generates correctly. SPs still do not show in MyMeta Browser, but a template that loops through them generates correctly.

Using the older Connector could be your quick fix, until the MySQL MyMeta code is fixed to work with the 5.1.x series.