That is usually called by differences in the changelog paths when you run liquibase update. The changelog name and path are stored in the databasechangelog table as part of the changeSet identifier and they need to match to be considered equal changeSets.
If you run “select * from databasechangelog” you can see the types of values that have been saved. Make sure both methods of running liquibase use the same changelog paths.
Alternately, you can use the logicalFilepath attribute to force the path used for changeSet comparisions, regardless of the actual path they have.