This is all ancient history now, I know, but thought I'd let anyone interested know for the record that there is no doubt the culprit for all the speed issues I have had is definitely the HDD in my laptop. I was recently using Calibre on my USB3 portable and to my delight everything mentioned in this thread whizzed along as it should! So now Calibre resides on the USB drive - not altogether convenient but also quite a good thing in that my library is now portable.
The abysmal (ABYSMAL!!) drive speed doesn't noticeably affect anything else I use, but it's agonizing using Calibre for anything beyond 2/3-book library modification/maintenance. Seriously, what's the use of Toshiba making a fast i7 machine then reducing it's functionality to WWII standards with the drive in it!!?