Just upgraded to Windows 8.1 x64 Pro via Windows Store, now I'm getting the "Secureboot isn't configured correctly" watermark. Looks like this is a common issue, no clear consensus on what to do. My feeling is that this an OS bug, never got that on Windows 8 and I didn't change any BIOS option. There's no SecureBoot option that I could ever find in my BIOS (and I did search), so I don't think there's anything I can do.
Anyone else getting this?
I got the same problem, however I found out that my secureboot had been disabled. (I actually remember doing it at one point.) After turning secureboot on again the watermark went away.
On a surface you can turn your surface off, then turn it back on while holding the volume up button. This will take you to the options screen for secure boot, re-enable it and then reboot and you should be good to go.
At least that's what fixed it for me.