Could it be you were faster when you enabled fewer cores? (I know some of my HT machines behave this way.)
What does your Resource Monitor show? All CPU's 100% loaded?
Any changes to system cooling?
I've played around with the cpu limit restrictions to no avail, cpu perfmon shows 100% load on all cores, and nothing has changed with my cooling
The only possible change....although it may have always been this way and I just never noticed it, is that there seems to be a slight increase in kernel cpu times if I enable that checkbox from task manager on the performance tab, sometimes I see red spikes which I'm not too sure to make of (but like I said, it may have always been like this):
Notice the green line at the very top of the CPU usage graphs indicates full usage on all cores...although it does seem to dip slightly when my client receives a new block.