Is there a way that only threads you read get marked as read? Whenever I log out any threads that I didn't read get marked as read and then next time I log on I forget what I haven't looked at yet. Obviously apply it only to threads that date back say, a week, so that every thread ever posted on BF doesn't get marked as unread.

That Software isn't "tweakable". And how it works totally depends on how you have cookies set in your browser. It'* not something we can tailor fit each person'* OS/Browsers/Settings/ even ISP (AOL in particular)