when JKDefrag opens via a task schedualer, the only way to make it an inactive window that is not on top of other windows is to hit the minimize button
Click the top bar of the new JkDefrag window once to make it active, and then you click again on other windows. It's a Windows idiosyncrasy, not caused by JkDefrag.
"hidden" from view
From the Frequently Asked Questions: Create a special userid (for example "jkdefrag") with administrator permissions, then add a schedule to the Windows Task Scheduler (see above) and specify that userid when asked for. The task will then run on that userid and not show anything on the user's screen.