Uninstall it.
Every single piece of software that requires you to reboot the machine during installation, has injected yet another component DLL into the system message chain.
It takes time to pass the zillions of system messages between these extra components. If one of them is brain dead or poorly written, keee-rasssshh time.
Better yet, use your 2nd drive to keep a GHOST image of the installed system. Start with fdisk and fresh install. Do only the Windows Updates, then image the system as BASE.GHO. Build the system modularly, and image it along the way. If you dork something up, restore from the previous image, instead of starting fresh from fdisk again.
Once the system is installed, image it again. Then, start turning off the various Windows services that are not required. Opus has an in-depth document that describes this. If you screw up, restore from the saved GHOST image. When the final system is completed, image it yet again.
This is a little off topic for hyper threading, but if enabling hyper threading induces system damage, it is best to have a current image to restore from.