The fix for CORE-1784 may apply to your problem even through you are seeing a different symptom. CORE-1785 will add the support you are looking for to create a single changelog across multiple schemas. It is implemented for the command line version so far, so the change just needs to be added to the maven plugin.
If you could send your sql to me nathan@liquibase.org I could make sure the fixes address your problem.
Nathan