Are you sure it's set up as IMAP and not POP3? You've actually gone and double checked the server settings and they are something like imap.google.com? Going off the idea that the simplest solution is usually correct, the simplest solution here would be that you have a POP3 setup, not IMAP. So maybe you want to triple check those settings.
Using Snow Leopard with all the latest updates. I have my Gmail account set up in Apple Mail as an IMAP account. When I delete messages in Apple Mail, the messages remain in my Inbox or Sent Items folder on the Gmail server -- if I log into Gmail via the web interface they are still in my Inbox or Sent Items.
If I delete messages using the web interface, they are also deleted from Apple Mail, so this is a one-way sync issue.
Is there a setting in Apple mail that will also delete messages from the server when I delete them in Apple Mail?

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