Download
Process explorer and run it as admin (it comes from Microsoft so its safe)
the default view is tree structure meaning like your task manager screen, it will show what processes are under System, but unlike the other one, it can show the hdd usage of each part so you can see what part of System is using the hdd. If you right click on the header, you can add extra columns - choose the I/O tab and add i/o reads & I/O writes
System process should be near the top of the tree view. Since i killed the process already I can't see anything using it on my screen.
This page shows what all the colours and headings mean, link at bottom of it shows how to use it to find problems. You can right click headers and run an av scan from within the program.