@Alwin Everything on your System Report seams fine. Have you altered your Cron Job Schedules in any way via a plugin? The only reason I would see this behavior happening is if your Network isn’t being “Auto Synced” prior to sending our the email. Basically the MainWP Dashboard has stale data when it’s fired off.
This is also being talked about here: Email notifications for updates are always outdated - #5 by pereffect