mail.app
Since a while back Apple Mail marks mail as read when searching. It's really bad when handling a large mailbox since it's easy to miss an email because you accidently marked it as read while searching.
Can anyone reproduce the error? When did it appear? Is there a setting to change it?
If I'm reading the initial question correctly, you wish to select which account new mail comes from.
In Mail prefs > Accounts > Account Information tab you can enter multiple email addresses in the Email Address field. You must separate them by commas.
When you create a new message The From dropdown will list every email address. These addresses will be used in the From: field.
The reason for this issue was the fact that I had set up the account as a POP account in apple mail.
When IMAP is selected the following screen appears:
and as can be seen the first item is the one I was looking for.
Drafts : Store draft messages on the server.
When the option above is not ticked the issue stops.
Best Answer
There is no setting in Mail to fix this problem. People have been notifying Apple about this bug since at least 2006. Obviously, Apple has no interest in fixing it. You can get plug ins to fix it. Truepreview, which is free, and Act-On from Indev.ca, which costs about $25. (Act-On's main purpose is to allow you to apply rules to messages as you send them.)
There may be others.