Looking over the Sandra(kudos for posting up front
), I see some possible red flags:
Integrated graphics are often a show stopper with PT
While nVidia graphics are preferred for an intel system, ATI might be a better choice for AMD(hopefully some AMD users will offer some advice here)
Wifi should be disabled when running Pro Tools(at least until you are positive that's NOT an issue)
This "ELBY CLONEDRIVE"....can you try disabling or uninstalling to see if it helps?
My 2 cents only, but I would have used the big 1TB drive as my audio/recording drive, and the 250GB drive for system. I would also have not done so many partitions(other than splitting the 1TB drive in half). While on the subject of drives and ironing out system issues, are you hip to drive cloning and imaging? If not, you need to be, so check out Acronis True Image, buy a sale-priced USB drive(like 1.5 or 2TB) and save images of your drives, especially your C: drive, and especially if you still are using Cubase on it(just in case things get wonky).