In Notes 6.5.x, when you reply to or forward a message, the message becomes unread directly afterward, even though you have already read the document.
This issue was reported to Lotus software Quality Engineering; however, it was been found that Notes was functioning as designed. To avoid the issue, enable the Database Property “Do not mark modified documents as unread” found on the Designer tab.

The property is enabled by default in the mail templates that ship with Notes/Domino 6.0.3 and 6.5.

A document that is forwarded or replied to in Notes 6.5.x appends a $RespondedTo field to the document and assigns it a value so that the corresponding “Action performed” icon appears in the view. With the addition of this field, the document has now been modified. Without the “Do not mark modified documents as unread” option enabled, Notes marks the document as Unread because the document was modified.

Lotus Software KnowledgeBase Document# XXXXXXX