Where Did My Messages Go?
Missing messages in Outlook? Getting new mail notifications but don't see anything in the Inbox? There are a few possible reasons for that.
One of the most common reasons is that you may have a filter set on your view that is hiding messages.
Most commonly we see that when people say "I opened a message and when I closed it Outlook deleted it!" Outlook didn't actually delete it, what happened is that you have a view selected that has an "Unread Messages Only" filter set - so Outlook is just hiding the read messages from you.
If you look at the status bar at the bottom of the Outlook window you should see (on the left end) a message that says "Filter Applied" if you have one.
To check on this click View (either the menu or the tab, depending upon your version of Outlook) and then click "Current View" or "Change View" (depending upon your version of Outlook) and see what view you currently have applied. Try to select a different view and see if that resolves the issue. The "Messages" view is usually the default and is a good choice, if you don't already have that set.
If that doesn't resolve it - and you still see "Filter Applied" listed - then you need to clear the Filter.
In Outlook 2007 and earlier go to View | Current View | Customize Current View (the steps might vary slightly depending upon version), click the "Filter" button and click the "Clear All" button on the dialog that appears. OK your way back out.
In Outlook 2010 go to the View tab of the Ribbon and click the "View Settings" button. Click the "Filter" button and click the "Clear All" button on the dialog that appears. OK your way back out.
Rules Moving Messages
It's possible that your messages are being moved to a subfolder by a rule.
If you go to the Rules Wizard (Tools menu or just on the Home Tab; depending upon your version of Outlook) check and see if you have any rules that might be moving your messages to a subfolder.
Sometimes you're just looking at the wrong folder. Scroll down in your message list (or press CTRL+6 to get the Folder list view) and see if you see ANOTHER Inbox folder. Are your missing messages in there per chance?
On the off-chance the messages actually ARE getting deleted, check the Deleted Items folder in Outlook. Are your missing messages there?
Multiple Machines Checking That Account?
It may be that you have a second machine - a home machine or laptop perhaps - that is also configured to check that same mailbox. If it's a POP account you may have that second machine configured NOT to leave a copy of messages on the server. Go into the properties of that account, through More Settings to the Advanced tab and check the box to "Leave a copy of messages on the server."
Another possibility is that AutoArchive is moving the items for you. Read more about AutoArchive