Ran again with the resource monitor up. Still followed the same trend, looking at the monitor, no real CPU usage, processes with disk were:
HDTune 50-110,000 B/s read
System very little
chrome.exe very little
Disk activity had a lot of small writes by "System" and not much else. Also this is all after a fresh reboot with all apps fully loading. What else could explain the stuttering coming on so suddenly and the poor disc performance now?