- What exactly do you mean that the HDD is being accessed? Is the only indication that the HDD light is flashing, or do you have another program open that is on the second drive?
I noticed that the mouse stutters sync up with the HDD light flashing most of the time. It happened during a download of a large file on Steam as well as during an antivirus scan of my system drive, and when I moved a big file between two drives the game isn't running on.

- How frequent is this issue? Every few seconds or only occasionally (or somewhere in between)?
It will happen every time one of the above processes is running, or when windows is moving files, defragmenting, loading another program or downloading larger files. During "normal" operation, when nothing but the game is running, it will usually not happen. But as soon as any other process starts (like an automatic windows update/download) the mouse will start hitching.

- Do you have a specialized mouse of any kind, or is it simply the mouse that came with the PC? Is it wired or wireless?
It's a wired logitech Proteus Core g502, with the latest Logitech drivers and software installed. I have tried using the default windows mouse driver as well as disabling the logitech software, but it didn't fix the problem.