OK, I think I've figured out what happens. Not every time, but maybe 1 out of 10 times when you shift-click to open in the default browser while viewing unread items only, the channel selection changes to a different channel. I think what I was doing is assuming the item I read came from the selected channel. Now that I know that happens, I've been keeping an eye on the selected channel before I do a mark as read.
You might want to see if you can reproduce this behavior. Like I said, it doesn't happen every time but it does happen probably 1 in 10 times.