Welcome to the forums,
Not quite sure what you're saying, when a mail item gets read it's just a metadata update in the DB.
Is your initial search query set to in:inbox is:unread by chance?
-Preferences tab (options on older versions) > Mail > Default mail search
-Preferences tab (options on older versions) > General > Show advanced search language in search toolbar
(Not common, but is it totally removed like zimbraPrefInboxReadLifetime set on your account?)
POP account somewhere?
What version are you using?
su - zimbra
zmcontrol -v
Or in the main search bar of the AJAX web-client type
$set:get version
http://www.zimbra.com/forums/announc...html#post62754