I had this same problem also up until about a week ago. I couldnt figure out what was going on to make this happen but i did fix it. What I did was unmount my HD's and then remount then. Strange as this sounds, it seemed to work. It went from literally 99.7% down to 3%..........weird. Anyway, give that a try, maybe it will help you as well
BTW - I'm not sure if you had this also, but my memory was being almost maxed out as well. I have 16G of ram and it was using 13.9G then, now its running at 265.4M. Substantially better
Good Luck!