The rule 'Hide non-billable expenses...' doesn't seem to work on all invoices. Why?
It is possible that this project was created before the rule was set in Global Settings. If any of the projects were created after the rule 'Hide non-billable expense entries on invoices' was checked in Global Settings, this rule won't apply on them as Global Settings is not retroactive. You need to add the project rule to the those projects in order for the expense entries to be hidden on all invoices. The best way to do this is to do a Batch Update to add the rule to all projects from the Projects screen.