Rules and misconfigured Junk Email filters are the typical cause of this.

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Robert Sparnaaij [MVP-Outlook]
Coauthor, Configuring Microsoft Outlook 2003
http://www.howto-outlook.com/
Outlook FAQ, HowTo, Downloads, Add-Ins and more
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> Did you ever find a solution to this issue? We are finding that
>> incoming emails are going directly into 'deleted items' instead of
>> 'inbox'. Can't find a settings fix, looking for suggested fixes.