Shortly after Windows 8.1 was released, some users noted that a new message would pop-up on upgraded devices saying, "Secure boot isn't configured correctly. Build 9600." The first report came on October 17, 2013 in a thread on the Microsoft Community forums HERE.
Microsoft has now released an update that fixes this issue on Windows 8.1 (x86 and x64) and Windows Server 2012 R2.
You can grab the updates from here: Update removes the "Windows 8.1 SecureBoot isn't configured correctly" watermark in Windows 8.1 and Windows Server 2012 R2