I have Mail 4.5 on 10.6.7 and a Google apps account.
My total message counts for each folder in Mail don't match the counts I see in the GMail web UI.
I don't have any custom labels or folders. I've tried rebuilding the mailbox in Mail, syncing the account, and switching the message view to "threaded". No dice.
Inbox, Sent, and Trash have always been off and Mail always shows more.
- Inbox: 62(GM) / 78(Mail)
- Sent: 88(GM) / 117(Mail)
- Trash: 199(GM) / 262(Mail)