You have have modified the time-zone of the hours on the built-in Schedules (5x13, 5x8, 7x24) in the Service Desk Tab -> Coverage Schedules page
After a re-apply schema, these hours are changed back from your adjusted times to the default PST time-zone
These built in coverage schedules are designed to be samples - to give you examples of what you can do.
Re-applying the schema will reset these back to their default values.
SOLUTION / WORKAROUND
Create new coverage schedules - these will not be affected / reset by the re-apply schema - only the built in ones will be reset.