Symptoms
Assume that you open the Options dialog box in Microsoft Skype for Business 2015 (Lync 2013) and change settings in the Persistent Chat section, such as enabling Show me an alert and Show the message in a new window for ordinary and high priority messages. When you sign out and then sign back in or restart the client, and immediately open the Options dialog box, the settings appear to be reverted to their default values, and the options that you checked appear unchecked.
Resolution
To fix this issue, install the December 6, 2016, update (KB3127976) for Skype for Business 2015 (Lync 2013). If the Options dialog box is opened before the client has connected in background to the Persistent Chat server, the Persistent Chat section of the Options dialog box will now warn the user that "Persistent Chat settings will be available later." Note Lync 2013 was upgraded to Skype for Business in April 2015.
