Hmm i can't say what right now but i think something else is at play here. Your GTX 1060 6GB and i5-4460 is a fine pairing the CPU shouldn't bottleneck it much if at all. You also have great storage drives and plenty of RAM.
My recommendations would be:
- Ensure your Nvidia drivers are up to date.
- Download MSI Afterburner and use the OSD to monitor temps on the CPU/GPU and usage on the CPU/GPU/RAM. If your CPU or GPU is getting too hot it will thermal throttle. Just want to check usage to make sure something isn't peaking at 100% for some unknown reason like CPU or RAM which could be an issue.
I don't think Power Supply would be an issue since the GPU is still working but if you could post the make/model of it i could take a look. Hopefully one of these helps
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