UPDATE : So I opened up the case and was cleaning out the dust from the components, when I decided, for whatever reason to try and swap the positions of both the cards after a bit of cleaning. I did so, cleaned up whatever I could and fired up the system.
Lo and behold, both cards are now running at x16 in SLI
I suppose sometimes the best fix is to just clean up the parts in your build
Here are some screenshots. Hope this helps anyone with the same problem.