Was the email that was marked as read highlighted in webmail? I believe there was an issue at one time where messages would come in and be selected, by default, and then marked as read even though nothing was done. To be honest, it's been awhile since 16.x came out, but I believe we changed that behavior at one point so that you actually had to interact with the message in order to mark it read.
If messages aren't being intercepted somewhere -- like in a client, on a mobile device, etc. -- that's about the only thing I can think of that may cause that behavior.
Derek Curtis
COO
SmarterTools Inc.
www.smartertools.com