Assume that you receive many incoming instant messages (IM) in Microsoft Skype for Business 2016 with tabbed or non-tabbed IM conversation mode. The taskbar icon only flashes for the first time when the IM arrives. It doesn't flash for the next immediate messages.
Note This behavior doesn't apply to the IMs that are received after around 30 seconds of the first IM. After that, any IM will be displayed in a new section in the IM window, and the taskbar icon will also flash.
To fix this issue, install the November 1, 2016, update (KB3127939) for Skype for Business 2016.