A user's modification to the wp-cron.php task setup by WP Toolkit is overwritten.
When the wp-cron.php cron option is enabled, modifications made to the cron job are being overwritten by WP Toolkit.
The WP Toolkit team is looking into this behavior further. Follow this article to receive an email notification when a solution is published in the product.
The user might consider detaching their site from WP Toolkit. There is an option within both WPTK-Lite and WPTK-Deluxe to do just that. Once detached, this should no longer be an issue.