In other words, the selectiong highlighting colour remains the neutral grey that is normally indicative of a selection that is in the background, even though the window is now in the foreground. And even if I click on the message again to confirm that it is selected, the selection highlighting colour remains the neutral grey that is normally indicative of a selection that is in the background.
Even in OS X 10.8.2, I’m seeing a bunch of bugs in Mail: read/flagged indicators that don’t update right away (and don’t sync at all from the iPhone), messages that can’t be marked as unread, and searches that don’t find the messages they’re supposed to.
I’m also seeing a new behavior when I receive multiple copies of the same message (e.g. as a direct recipient and via a mailing list or two). Mail seems to silently delete one of them! I can see two messages in my iPhone’s inbox and watch one of them disappear when I open Apple Mail. This has made it difficult to test some mailing lists that I administer, as Mail was deleting messages that really were not equivalent.
See also: Replying From the Proper Account.