The most prominent processes, which will hurt disk accesses are anti-xxxx programs. Even when allowed, they still interfere with any application which is accessing the disk.
You can run the resource monitor (bring up task manager, under "Performance" tab and hit the "Resource Monitor" button) in Windows and check it when you note disk access to see what program is running at that moment. It will show in the "Disk" tab.
If you are running a dynamic swap area for Windows, that will take more resources, than a fixed sized one. If you have multiple disks, you can put a swap partition on each, which helps also.
Fixed size swap areas are guaranteed to be contiguous (much faster for reading and writing) whereas dynamic ones are spread all over the file system in any hole the operating system can find.