When reverse engineering a database running on Linux using MySQL the foreign keys are not included. I am running MySQL 5.0.48 on Linux Red Hat Enterprise Linux Server release 5.1 (Tikanga). Using the native connection the fk’s are not reverse engineered. When using the ODBC (version 5) the fk’s are displayed and engineered. Using the native connection in 2.25 also fails to display the fk’s and 2.25 does not seem to work with MySQL ODBC 5 version. Seems like a bug that using Native Connection does not completely reverse engineer.
Reverse Engineering using the native connection on older versions of MySQL (5.0.45) does include the foreign key connections.