A couple of weeks ago all my email starting showing up black instead of red and my Inbox doesn’t show a number with the number of new emails received e.g. Inbox (3). Under tools, preferences, colors all my sender colors are default, so it isn’t that. Any thoughts? Thanks.
Subject: Lotus Note 6.5 - Unread email is always black
Matthew,
I am not sure if you have solved this problem, or not.
In the case of an agent that is accessing all documents, an undesired result maybe that unread marks will be modified from unread to read.
You may elect to do one of two things:
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Identify and disable the agent.
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Enable a different db property: “Do not mark modified documents as unread”.
Hope this helps,
Ben M
Subject: Lotus Note 6.5 - Unread email is always black
Do you have unread marks disabled? Check the last tab of the database properties.
Subject: RE: Lotus Note 6.5 - Unread email is always black
No Charles, the “Don’t maintain unread marks” box is unchecked and the “Replicate unread marks:” is set to “All servers”
Subject: RE: Lotus Note 6.5 - Unread email is always black
Okay, just checking 
You might want to try this:
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Close your mail database
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Remove the mail icon from your workspace
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Compact your workspace
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Close Notes
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Delete cache.ndk (in your Notes\Data folder)
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Restart Notes
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Open your mail
If that doesn’t clear it up I don’t know what else to suggest.