Symptoms
Assume that you have several undocked conversation windows (free-floating windows that don't appear as tabs in the tabbed conversation window) with different widths and heights, and you check the Reopen my conversations when I sign in option in the General section in the Options dialog box in Microsoft Skype for Business 2016. After you sign out, and then sign back in Skype for Business 2016, those conversation windows are restored, and they are all restored by using the same width and height.
Resolution
To fix this issue, install the January 3, 2017, update (KB3128049) for Skype for Business 2016.