Mail Icon in bar not synced with Mail which I log into thru Mac Mail

Clicking on the Mail icon in bar gives me a list of emails in alphabetical order, going back years. I'm certain I've deleted many of these, but they're still there. No mail received recently goes here - the only way to get my mail properly is to log in to MobileMe using passwords etc [before that, Mac mail] which can be tiresome if I just want a quick check.
How can I sync these two, so that whatever arrives/ is deleted /is sent appears in both locations exactly the same?
Thanks 4 any advice.

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