PerfectIt checks your final text, so while PerfectIt is running, the document should be set to 'Show Final'. You can still track all changes, they just should not be displayed while PerfectIt is running.
If you are working in Word in track changes mode, then you should run PerfectIt 5 in 'Revisions Mode'. This will ensure that revisions are automatically hidden when you start PerfectIt's checks and that they will re-appear when PerfectIt is closed.