GPU usage low in Skyrim (Modded) while performance suffers ~

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I don't seem to be having much luck with my PC as of late. Most games seem to stutter in some way shape or form.

I modded my Skyrim for the first time earlier, installed a few but nothing remarkably major. The performance hovers around 40fps looking in certain directions and shoots up to the VSYNC cap in others.

I monitored GPU usage and both GPUs (Specs in sig) are sitting at the non-boost state of around 800-something MHz on the core. The temps are sitting around a mere 50-60c and the fans are running on neither card. All in all these things should be performing far better and for some reason they're not.

CPU usage shown in Task Manager only sits around 20-30% from when I've caught it doing an Alt-Tab. 1 core is utilised about 80% going by the graph and the rest poodle along at about 20 or so %, if that. Temps for the CPU remain at a chilly 40c. I realise Skyrim is a heavily CPU-bound game, but an overclocked 8350 can't be this bad, surely?

This wouldn't even be an issue exclusive to Skyrim. Crysis 3 (While demanding) also has some issue with massive frame stutters with physics related things, best way I've found to test this is to shoot breakable tree's. Giant lag spike every time.
On Crysis in particular I attempted to narrow down the issue a while back by disabling my overclocks one by one. Lowering settings etc... Same on everything.

This machine exhibits none of this behaviour when running stress tests, gpu benchmarks or any other kind of synthetic program.

The games are hosted on a mechanical drive, if that makes any difference. Tested the speed for it and everything's normal.


Anyone know what's going on? I keep putting it down to bad optimisation or poor drivers, but that's more of a cop out for my sanity. The frame drops on certain games are annoying me too much to continue ignoring it.