Line marker
Whenever you close or minimize a window, the line marker marks the spot where new messages come in to a channel or query window. This allows you to scroll back and easily see which messages you've missed. You can press Control+L to scroll back to view the line marker. The line marker is only updated after you've scrolled back to view it.
In other words, if the window is your active one (where you have the cursor) the line marker wont be activated and if you dont scroll back to it, it wont be reset.