I do tend to see generateChangeLog as a way to bootstrap using liquibase, but not the primary workflow and so there does tend to be more edge-case issues like handling cross-database foreign keys in mysql. The best way long-term to work with Liquibase is to add to the changelog file yourself during development.
However, the generateChangeLog command shouldn't completely die in this case. There is a --schemas parameter that can be used to make Liquibase snapshot both schemas/databases which may help since it will see all the objects. Otherwise, open a but a liquibase.jira.com and I can take a look at it more.
Nathan