Arcadius

Seeing how your Wifi speeds are also being limited, and you NIC is already negotiating at 1Gbit, my only guess would be that it's something on your windows install, maybe some software limiting download speeds for some reason?
 
Try a linux usb stick as previously mentioned, or do another windows install in a different disk/partition just to be sure.
 
Or try booting into safe mode.

Man, you've got a real belter of a problem!
 
Try booting a Linux distro (Ubuntu) as @GuiltySpark_ suggested. I'd love to see what Linux thinks of it.
 
Windows reporting a 1Gbs connection and I'm assuming the led on your NIC / Switch / Router is flashing Amber (Not Green).. I think that's the correct way between 100 and 1000Mbs.
 
The only thing I can think of is some kinda mobo fault that's limiting the link speed of the PCIe lane(s). But this only holds true if its the same pipe for the integrated NIC, Wireless adapter AND external NIC you've bought.
 
Tough one buddy!

Unfortunately I have both with the old one and this new one
 

Yes I understand the difference between Mb and MB my dude...