Based on you saying DX9 launches, but graphics are missing...I would say that it may be corrupt game files, but even with a re-download it doesnt fix it?
Are you using the normal PC version or the steam version?
Have you tried completely reformatting the drive? It might be that the game is using leftover data from install to install.
Have you tried installing the game on a seperate/another drive?
Have you tried manually re-installing DX11 from microsofts website?