The foreign keys are between InnoDB tables? I don't remember off hand if myisam stores FK metadata even though they don't support FKs.
Also, are they between tables in different databases/schemas? Or all in the same database?
Unfortunately the DBEngine is database-specific functionality that is not captured in liquibase and so needs to be added yourself. The generateChangeLog logic tries to handle normal cross-database features but doesn't yet get into more unique attributes.
Nathan