I'm running Win 8 RTM and was able to get 12.0SP2 working with a DE0-Nano after installing the stand alone programmer.
The usbblaster inf does not seem to properly load some files but it was the jtag server that caused me problems. The Altera dlls are a few months older than the latest FTDI files but that does not appear to be the issue with the install.
I installed and run without setting "run as administrator" or using compatibility mode for the applications.
I did not uninstall the previous driver when installing the stand alone programmer.
I'd expect similar behavior from earlier revs (pre-release) of Win 8.
What release version are you running?
Most releases will ignore installed drivers (even signed) on an over-install because the security policy has changed. I'm guessing that you are running an older version of Quartus. Even 12 does not have a properly published installer but that only generates a warning. Thankfully the drivers are signed.
-Dan