One of my fellow System Administrator complained about few emails which he never received, like the mass emails sent within our company. He also never saw any mails generated from system like alert emails. At one time, he said he saw an email briefly on his Windows Mobile and it’s gone mysteriously from his Inbox.
Finally he figured out himself. It’s his Outlook Junk Mail settings found under Outlook:Tools–>Options–>J-Email–>Junk E-Mail Options. He had checked "Permanetly delete suspected junk e-mail instead of moving it to the Junk E-mail folder" check box.
When I think about this option, I think Outlook displays Junk E-mail options for the first time you receive an suspected junk e-mail. By given brand new Outlook software to a user, It’s more likely users may wanted to delete the Junk e-mails right away.
But user always learns in time that it’s better to deliver the junk e-mails to the "Junk E-Mail" folder for later review. Mostly some legitimate email ends up in Junk Email folder for many reasons. You may want to review the Junk emails once in a while and mark the needed emails as safe.