I updated to Lion and now the Search function in Apple Mail is not working properly

Even though the "All" option is selected, when I type a string in the Mail spotlight search box, the string is not found. But I know for a fact the string is in an email and I've manually found the email (in a folder) and copied and pasted it into the search box. Mail is still not able to find it.
I have also checked to make sure that "Message contains" is the option in the search box. I've noticed that in some previous searches there has been a little arrow dropdown option next to the magnifying glass icon. But that arrow is not showing up consistently...and is not showing up now.
What am I doing wrong?

Ok...here's the steps to fix this as efficiently as possible. I have a whole bunch of mailboxes under "On My Mac" and they have a bunch of mailboxes nested in them. I get my messages into Apple Mail via IMAP. (I don't know if this matters.) The steps below assume you have a similar setup.
1. Hold the Option key down and click the dropdown arrow next to each mailbox that has one. This will cause all nested mailboxes below it to appear.
2. Go to the top of the list of mailboxes under "On My Mac" and highlight the first mailbox. Then hold the Shift key down and highlight the last mailbox in the list. This will cause all of the mailboxes and nested mailboxes to be highlighted.
3. From the menu, select "Mailbox --> Rebuild" and the rebuild process will start.
4. Watch the top of the mail screen to see the message count change as the mailboxes are being rebuilt. Wait until the activity stops before doing the next step.
5. As the mailboxes were rebuilt, many messages were reset as "Unread" even though every message was previously "Read." Make sure the mailboxes you want to affect are still highlighted. Right-click and select "Mark All Messages Read."
That fixed the problem for me.

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[click on images to enlarge]
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