When you pair a Polycom VVX telephone with a Better Together over Ethernet (BToE) application, a Lync 2013 (Skype for Business) credential prompt is generated. However, it comes up behind all other active windows. Therefore, you are not aware that you need to input the credential.
To fix this issue, install the November 1, 2016, update (KB3127934) for Lync 2013 (Skype for Business).
Note Lync 2013 was upgraded to Skype for Business in April 2015.
The third-party products that this article discusses are manufactured by companies that are independent of Microsoft. Microsoft makes no warranty, implied or otherwise, about the performance or reliability of these products.