There seems to be a bug with the "Mark as Read" preferences. If "Mark on Click Delay 0.5 Sec" is set, deleting a message from the top of the list will move the selection to the next message (as usual) but the next message won't be marked as read.

I believe it is a bug because it doesn't happen with the similar option with 1 Sec or 3 Secs delays (on those cases, the message that is selected after deleting one will be marked as read).