Problem:

For clients who use Active Directory Federated Services (ADFS) as their federated identity provider, when clicking on Jira hyperlinks embedded in documents from within the following Microsoft Office products:

• Word
• Excel
• PowerPoint

the chosen Office product may appear to hang for 60 seconds and (Not Responding) may become visible in the title bar before the page successfully loads in the browser.

The problem is not evident when clicking the same links in Outlook. 

Cause:

Microsoft Office products (except Outlook) cannot share the token/cookie used by Internet Explorer. 
This is a known limitation of the Office product line, it attempts to contact the site and meets a credential prompt. Because the credentials prompt is a website it cannot be displayed by the Office product.
At this point, the program will appear unresponsive for the 60-second timeout. 

Outlook uses a different way to interact with IE than the affected Microsoft Office products.

Resolution:

There is unfortunately not a complete resolution to this issue at the time of writing this article, the problem lies within the Microsoft Office product and Microsoft is aware of the issue. 

To stop the unseen authentication prompt you must hit your ESCAPE key after clicking the NetDocuments hyperlink. This dismisses the prompt and skips the 60 second timeout period and just opens the link in the browser. 

Alternatively, copy and paste the URL to the browser as necessary. 

The problem is only noted with ADFS authenticated sites; other single sign-on (SSO) solutions are not similarly affected.