A few things to check:
* Overall processor usage will be low because you have 8 cores and not all of them are going to be utilized by Dolphin + the OS. You need to use a utility to check whether the clockspeeds are going up to their maximum while Dolphin is active. It may also be a good idea to set your Windows power profile to "High Performance" as this should limit the throttling the occurs when the computer perceives that it is idle.
* I have seen GPUs not going up to full speed on Dolphin. I had some weird stuttering issues that I isolated to my Radeon 7950 not going up to its full speed dynamically fast enough; basically, at the start of a demanding graphics scene the GPU would still be running at its desktop speed, i.e., 300 MHz. You can check for this with something that logs GPU speeds and utilization, such as GPU-z. For AMD, I have been using RadeonPro to force max GPU clockspeeds when dolphin is running. I'm not sure how to do that on nVidia.
* You say that you are running 4.0.2, but then say that the windows says: 4.0-1244. To me, that implies that you are running a developmental version. Does the same issue occur on the stable 4.0.2 version? Have you tried fully deleting Dolphin settings to reset everything to default? I also noticed a weird stuttering issue when running a recent dev version in parallel to 4.0.2. I don't know enough about Dolphin's internals to explain why it happened, but it seems like settings are now centrally stored, so it seems like a conflict is possible if things change. Maybe this is due to the shadercache being incompatible and needing to be regenerated with different versions?
* Overall processor usage will be low because you have 8 cores and not all of them are going to be utilized by Dolphin + the OS. You need to use a utility to check whether the clockspeeds are going up to their maximum while Dolphin is active. It may also be a good idea to set your Windows power profile to "High Performance" as this should limit the throttling the occurs when the computer perceives that it is idle.
* I have seen GPUs not going up to full speed on Dolphin. I had some weird stuttering issues that I isolated to my Radeon 7950 not going up to its full speed dynamically fast enough; basically, at the start of a demanding graphics scene the GPU would still be running at its desktop speed, i.e., 300 MHz. You can check for this with something that logs GPU speeds and utilization, such as GPU-z. For AMD, I have been using RadeonPro to force max GPU clockspeeds when dolphin is running. I'm not sure how to do that on nVidia.
* You say that you are running 4.0.2, but then say that the windows says: 4.0-1244. To me, that implies that you are running a developmental version. Does the same issue occur on the stable 4.0.2 version? Have you tried fully deleting Dolphin settings to reset everything to default? I also noticed a weird stuttering issue when running a recent dev version in parallel to 4.0.2. I don't know enough about Dolphin's internals to explain why it happened, but it seems like settings are now centrally stored, so it seems like a conflict is possible if things change. Maybe this is due to the shadercache being incompatible and needing to be regenerated with different versions?