There was a poster on a forum recently who was puzzled about disk activity on his system. He had created his database files on non-system drives, yet when he checked the activity on the C drive, it was constantly thrashing. As SQL Server was the only application of any note on the system, he was wondering what on earth was going on.
There are things in the OS that will write to the drive but I think the most likely candidate is that tempdb is still on the OS drive.
In recent versions of SQL Server, if you don't change the location of tempdb, it'll end up where the SQL Server programs are installed, and that's usually on the system drive.
Moving tempdb to another drive is easy and is described in this article.
There is a specific example near the bottom of the page that shows how to move it.
There is one more possibility that immediately comes to mind, and that's if there's not enough memory on the system and the Windows OS page file is thrashing, but that's far less likely.