Apple Mail 6.0 In Box now includes messages moved to other folders

All Mail converstions with the same subject appear with a new message in my In Box eventhough many of those emails with the same subject have been moved to another Mail Box.  For example, I use Salesforce.  Thoughout the day I will receive emails with the subject "A lead has been assigned to you".  After I have delt with these leads I click on the trash can and delete these messages.  Now after installing Mountain Lion with Apple Mail 6.0, in the Preview screen I see the emails that are in my In Box plus all other email with the same subject.  In this case there are sever hundred.
How do I get my In Box preview to just show the current messages and not messages in other folders with the same subject line?

You are correct that this changed with Mountain Lion.  I have one Mac still running Lion and when I checked it the "Include Related Messages" box is not checked.  So I assume that the upgrade to Mountain Lion checked this box during th upgrade process.
I have experimented by unchecking and checking this this option to Include Related Messages.  One feature I like is if I have replied to a message the sent reply appears shaded above the message I have replied to in my In Box or any folder/mail box where I move the message.
Bottom line, now that I am getting use to the change, I like it and will leave the Include Related Messages box checked.  The only drawback I see is that unrelated messages that have been moved to other folders and are not really part of the thread appear in the threaded message.

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