Mail bug - Mail insists I have unread messages when I don't

I just purchased a new MacBook Pro and copied all my mailbox contents over from my PowerBook G4 via a Time Capsule backup of my entire user folder.
Last night, after checking for new mail, Mail said I had 40 new messages. But when I got done looking at all of them, Mail still showed (in the ovals next to each account inbox and the red dot on the dock icon) that I had 20 unread messages. It also flagged more than 600 messages in Trash as unread, as well as a few in Junk.
Nothing I do can convince Mail I have read all my messages. I experienced this problem intermittently on my PowerBook, but there, whenever I clicked on the relevant account inbox and Mail checked and saw I had no new messages, the numbers all disappeared.
I get a lot of mail throughout the day, so knowing how many messages I have at any given time is important. How can I make this problem go away, short of deleting all my messages and starting over (not feasible as I constantly refer to and rely on these messages).

My PB just crashed with a kernel panic and when it came back it said something about the mail being corrupted and had to import all my messages. That all seemed to work fine, but I had 12 unread messages in the dock icon I couldn't get rid of. I read through these discussions and found the unread smart mailbox trick and that found some of them, but I still have four unread messages (according to the dock icon) and nothing shows up in my unread smart mailbox. Any other suggestions?
Thanks.

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I hope this is the right place to put this!
I recently updated my 5800 xpressMusic. I honestly thought It was updated but it went from something like Version 20 to 50
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Why does Mail keep showing that I have incoming messages, when I don't?

...usually hundreds via the "burning cigarette"!

Quit Mail. Force quit if necessary.
Back up all data. That means you know you can restore the Mail database, no matter what happens.
Triple-click anywhere in the line below on this page to select it:
~/Library/Mail/V2/MailData
Copy the selected text to the Clipboard by pressing the key combination command-C. In the Finder, select
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A folder window will open. Inside it there should be files with names as follows:
Envelope Index
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Move those files to the Desktop, leaving the window open. Other files in the folder may have longer names that begin as above. Move those files, if any, to the Trash.
Log out and log back in. Relaunch Mail. It should prompt you to re-import your messages. You may get a warning that the index is damaged and that Mail has to quit. Click OK. Warning: The process may take hours if you have gigantic mailboxes. For reasonable-sized mailboxes, it should only take a few minutes.
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Date: Mon, 3 Sep 2012 19:48:31 -0600
From: [email protected]
To: [email protected]
Subject: I had to reinstall CS4 and now have error messages when opening bridge and photoshop
    Re: I had to reinstall CS4 and now have error messages when opening bridge and photoshop
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Go To Help->Updates and install the latest update. It should work.
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Rocketman

Quit Mail. Force quit if necessary.
Back up all data. That means you know you can restore the Mail database, no matter what happens.
Triple-click anywhere in the line below on this page to select it:
~/Library/Mail/V2/MailData
Copy the selected text to the Clipboard by pressing the key combination command-C. In the Finder, select
Go ▹ Go to Folder
from the menu bar. Paste into the box that opens (command-V), then press return.
A folder window will open. Inside it there should be files with names as follows:
Envelope Index
ExternalUpdates.storedata
Move those files to the Desktop, leaving the window open. Other files in the folder may have longer names that begin as above. Move those files, if any, to the Trash.
Log out and log back in. Relaunch Mail. It should prompt you to re-import your messages. You may get a warning that the index is damaged and that Mail has to quit. Click OK. Typically, the process takes a few minutes, but it may take hours if you have gigantic mailboxes. In that case, you may be able to speed things up by temporarily adding your home folder to the Privacy list in the Spotlight preference pane. Remove it when Mail has finished importing.
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Any ideas?
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David

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Mail bug - Mail insists I have unread messages when I don't

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