Okay.. So I just re-tested.. At first it didn't work.. Initially I had the exact same issue. (only opposite) When the the customer was not notified, the legend seemed to indicate that they had been..

I knew that the FEC add-on had code in it's super_orders.php file to correct the notification issue as well. So I was installing FEC anyway so I used Winmerge to merge the FEC code into the super_orders.php file. I grabbed the notification code from the FEC version of the super_orders.php file and replaced the rev 47 notify code, and it now works with the correct legend flags..

Not gonna do it now, but I'll have to go back and do a vanilla install of Zen and Super Orders to see what I did to break the Rev 47 super_orders.php file.