See this thread. There are several different suggestions spread through this thread, including a PowerShell script provided by logos. You should be able to get them working with one of those solutions. I would try the PowerShell script first.
The part of the thread with the Powershell 'fix' is https://community.logos.com/forums/p/105737/735038.aspx#735038 but you should read other posts, particularly if you installed 64-bit Office. But if you are using Office 2016 you will have to wait for Faithlife to fix Smart Tags.
I may give that at try when I have time to kill. Until then I hope Logos comes up with a fix so their software will cooperate nicely.
The Powershell post is the fix! The issue arises when upgrading from Logos 5 (32-bit) to Logos 6 (64-bit) but also arose in Logos 6.3 when Faithlife introduced a different method to update the application.
This morning when I start Logos it wants to update first, which was the cause of may problems. Other than clicking the "No" button every time, is there a way to turn the updates off?
You can delay updates by setting Automatically Download Updates to NO, but there is no way to prevent that without going offline.