The Differences window does not show all the files that are copied, deleted, moved, etc.
Check to make sure you have not filtered out some of the files from the Differences window.
When the profile is next run, and the Difference window appears, click on the Filter tab/menu and enable:
Show files/folders not on Source/Left (*)
Show files/folders not on Destination/Right (*)
Show changed files
You may also want to tick the menu item "Show skipped files/folders" and "Show files skipped due to rename".