When you send an email to the user and it does not show up in his/her Inbox within outlook but if you perform an advance find on the mailbox you can see all the messages but the location would be "Top of information store"
All you have to do is use MfcMapi and clear out the rules because that might be causing the issue.
1. Create an Outlook Profile for the affected user's mailbox in Online Mode.
2. Run MFCmapi.exe.
4. Select Session -> Logon and Display stores.
5. Select the outlook profile for the concern user and click OK.
6. Select Mailbox - right click Open Store.
7. Expand Root Container.
8. Expand Top of Information Store.
9. Right click Inbox and select "Open Associated contents Table"
10. Under "Message Class" column delete all the entries with display name "IPM.Rule.Message" and “IPM.ExtendedRule.Message”
11. Close MFCMAPI and re-open Outlook