I am receiving similar complaints from a set of my SM customers.
SmarterMail Enterprise Edition
My mailbox does not exhibit the behavior. Not all users exhibit behavior. But some users are seeing it. I watched it on a customers' mailbox yesterday where the message changed from unread / read after the user deleted a previous email and then SM repositioned in the list of messages pane.
My customers are begging me to have this work like MS Outlook where you can configure webmail (My Settings) to go to read only if the user double-clicks on a message.
Apparently, there used to be a setting which perhaps helped with this. This is from SmarterMail 10.x Help:
Enable automatic mark as read for previewed messages - Select this option to automatically mark previewed messages as read.
However, this setting does not occur in v11.x. I cannot find it under My Settings.
I think this may be occurring due to some sort of synchronization between a mobile device and SmarterMail. The user who is exhibiting the issue has a new Samsung Galaxy S5. My mailbox is not exhibiting the issue and I have an iPhone 4 (with fetch every 30 mins).
I have multiple users complaining about this behavior and saying they are missing messages because of this read/unread indicator issue.
The read/unread issue is in the webmail interface.
I am going to work with the users to try and narrow down what may be affecting the behavior. I'm leaning towards mobile device or browser issue.