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I think the problem could be the VRMS on your Motherboard are overheating, due to the increased power draw since you updated your 6 core CPU to an 8 core. I checked your Motherboard and it does not have any heatsinks on the VRMS, please refer to the picture below.
Use HWINFO64 to monitor the CPU Package temperatures. Download HWINFO 64 http://www.hwinfo.com/download.php
If the CPU package temperature gets up to around 65-70c, then the Motherboard VRMS could be overheating, this will cause the CPU to drop to the lowest clock speed momentarily and could explain your sudden FPS drops. You can measure the temperature and CPU frequency using HWINFO to check for fluctuation.
Thank you for your reply, and the help is very much appreciated. I do however need to correct one small thing, it wasn't the CPU that was updated as I always had the 8 core FX-8350... It was the GPU that was upgraded from R9 280 to RX 480. Dismissing the minor misunderstanding your reply is still very much appreciated and will still check the temperatures if incase that could be an issue but I would mostly think its to do with the new GPU or even the drivers for it ect.
I am also looking into the idea that my saved games are played from a desktop external hard drive too, so even that can be a cause. If you have any other suggestions please feel free to let me know as I've not yet figured out the cause to my frame drops yet.
I will later on reinstall one of the games to the computer c: drive to see if it runs smoother without frame issues...
Perhaps you can try running some benchmark like Furmark, 3DMark, instead of re-installing the games. See if you get the periodic slowdown, and check temperatures of system, CPU and graphic card.