accountsmail.app
I recently picked up a used Macbook Pro with Lion installed.
There are no other accounts in the native Mail app except my new Gmail one.
However, when I send an email, the "Reply-to" address that the recipient sees is the email address of the previous owner.
I cannot find a way to remove this email address, it is not in the settings of my sole Gmail account. It seems to be registered somewhere in the account info of the Mac.
There is a preference you can set so that composing a new message defaults to a specific mailbox rather than the currently selected mailbox.
Replies go from the account to which the message was addressed. I'm not sure how it breaks a tie if both of your addresses are included or copied, but you can always override the "from" account by clicking on your name / email under the subject field.
In the message composition window, there's a pulldown above the message body, on the right, to select which email address you're sending from. The default for this depends on which mailbox you have selected in the main Messages window. It sounds like you're doing this.
If you're sure the above is being done for sure, then it's possible some gmail filters or tagging is getting in the way and making it look as though the reply lands in the inbox for one when really it's in another.
I would check the webmail and see if the issue is also seen there. If it is, then you're likely not sending from the right account, even if you think you are.
This may be because a certain account is locked into a particular SMTP server.
Mail -> PreferencesAccounts tab.
Best Answer
Check the "me" card. Open Address Book, go to the "Card" menu, and select "Go to my card". Edit if required. Restart Mail, and send yourself a test email. Check the from address.
Also, I know you've already checked this, but please check again. In Mail.app, go to Preferences, Accounts, and make sure that the email address is set correctly.