Out of interest, what Nvidia Drivers are you using?
I have exactly the same issue as fitzcarraldo.
NVControl Panel AND Inspector will not apply any settings to SH5.
(even something simple like VSync won't apply)
My personal setup:
Uplay digital SH5 patched to 1.2
GTX 670
Driver 314.22
I have tested EVERY WHQL driver set that supports my card, some 7 in total going back to May 2012. None of them will force settings to SH5.
Unless I can fix this, this bug ridden POS game is going back to gathering dust.
I have one last thing to attempt. Take Uplay out of the equation, I am quite prepared to believe that NV can't detect the SH5.exe application when it's launched by a third party app. As daft as that sounds.