Why would emails get stored in user’s Mailbox folder rather than Inbox

Good morning,
I’ve an Outlook 2003 issue where one of our users could not find messages in her Outlook 2003 client Inbox folder. Upon furthur invegstigation we found email stored at the Mailbox level folder (Mailbox – Username). Instead of Outlook Today, she has a lot of stored email she never read. I moved it all to her Inbox, but does anyone know how this could be fixed so no more email gets stored there. Right now I have set up some rules, but that seems real band-aid like.

Also on her client I right clicke her mailbox folder, selected open, and Outlook Today is now showing like everyone else.

Any advice would be appreciatted.