A user's modification to the wp-cron.php task setup by WordPress Toolkit is overwritten.
When the wp-cron.php cron option is enabled, modifications made to the cron job are being overwritten by WordPress Toolkit.
The WordPress 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 WordPress 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.