For me, long ago meant that before the forum change, reading an IE message meant that the comments and the original message were marked as read, and did not show up in the new message box on the right hand side when that page opened.
Right after the forum change, the original message remained unread, and the only way to clear it was to use the options menu to mark as read.
Now, sometime since last week, the original message gets marked as read after reading it, except as Tim said, there seems to be something like a race condition with the counter. The forum recognizes the original and the comments as having been read, but it seems like not until right after the message thread loads. The message thread that I opened up still shows itself in the new message box, which is now located on the left side of the screen.
