The System process is a file which stores information related to local hardware settings in the registry under HKEY_LOCAL_MACHINE.
I have no idea why yours is taking so much CPU time... but leave it be.
Btw, next time you run a HT scan [yours is clean] you could fix this one:-
O4 - HKLM\..\Run: KernelFaultCheck]%systemroot%\system32\dumprep 0 -k
- you had a crash some time ago; this is just the dump of it.
Of course, some trojans name themselves as common processes to hide in plain view.
You could try this scan- download RootKitRevealer from http://www.sysinternals.com/Utilities/RootkitRevealer.html [the link is at the bottom of their page] and place in a new folder. Read that webpage. Close all open windows, shut all applications, and then open a Windows explorer and Run RootKit Revealer from its folder...[dclick the .exe file]. Do not touch anything, even mouse, until it completes its scan.
Another free online that is excellent is Pandactivescan. Follow the leads from this webpage:-
http://www.pandasoftware.com/products/activescan?