Incorrect number in dock icon

This is a recurring problem: the red dot number in the dock displays a different number of emails in MAIL compared to when I check MAIL online through my .mac account.
Sometimes it is junk mail, but sometimes it is regular mail. What I mean by "regular mail" is that I will receive an email (and a red dot) from William in the morning. Then I will have no red dot all day. Then William calls to say did I get his email which I did not. Then I go online to check MAIL through my .mac account, and LO! there is William's email as well as a few others that did not "go through" to my desktop MAIL.
I've performed the steps (months ago and many times since then) suggested in this older posting:
http://discussions.apple.com/thread.jspa?messageID=721034&#721034
It worked for a few days, but the problem persisted.
And have also rebuilt regularly as well as cleaned up my mailbox so that mail isn't overstuffed.
Is anyone else having this problem or can anyone help me to understand why this is happening?
Thanks,
Genie

Just clicking on the icon in the Dock causes Mail to update the unread count? And Mail keeps ignoring the new messages even after selecting the mailbox and doing Mailbox > Rebuild?
Let's check first whether there could be a rule that has a bearing on this:
1. Quit Mail.
2. In the Finder, go to HOME/Library/Mail/.
3. Locate MessageRules.plist and move it to the Desktop. If there is a file called MessageRules.plist.backup, move it to the Desktop too. You may also see MessageSorting.plist files there; this is where Mail 1.x stored the rules, and they are no longer used by Mail 2.0, so just move them to the Trash if you see them.
4. Launch Mail. Go to Mail > Preferences > Junk Mail, enable junk filtering again, and configure it however you wish. You may want to shut down the Internet connection before launching Mail to prevent it from downloading anything until the junk mail filter has been enabled.
If the problem persists after doing this, then you know the rules have no bearing on this, and you may move the files on the Desktop back to the HOME/Library/Mail/ folder, overwriting any files Mail may have created anew there (quit Mail first).

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