The VIA will ensure that you are able to flash any drive without issue (vendor intro error messages) on any motherboard. But using the onboard SATA should be more stable than using the VIA when it comes to freezing issues.
To fix freezing problem: Does your computer freeze when both CK3 + Drive SATA cable are plugged in, or when only the CK3 is connected? I guess you might have to still download and install the latest JungleFlasher
http://jungleflasher.net/downloads.html and finish outroing your device from there. Windows doesn't know the best drivers for an Xbox 360 DVD drive to install and so it will freeze randomly since it thinks it is faulty hardware, but sometimes it will work if you keep restarting Windows and JungleFlasher.
Some computers can freeze since the CK3 is sharing some of the power from your power supply. Try disconnect some devices like an optical drive(s). It could be either the CK3 or the Xbox DVD drive that your computer doesn't like being connected. It should work after a few restarts. If not, turn on the CK3 only when Windows boots up fully. Select correct I/O port in JungleFlasher, etc. and do the Outro / ATA Reset.