This happens randomly, and is only resolved if I reboot my computer a bunch of times. What happens is, everything becomes sluggish and laggy. My CPU usage spikes up for no reason, and my FPS in games are low. Videos also become pixelated sometimes. As far as I know, this only occurs after booting up the PC. If the PC has been on, I don't believe it will happen. But once it does happen, it's like that till I restart a ton of times. I'm like 99 percent sure it isn't malware, I've run scans with Kaspersky Total Security 2016. Though what I do find weird is when the CPU usage spikes to 100, there are no procces using any usage at all really.
Videos of it happening:
(Notice how everything is stuttering/lagging, the YouTube video is becoming distorted, and my CPU usage is at 99 percent)
Two SSD's and One HDD