Think this is all related to our storage drive getting locked, the files were unable to be written to the temp directory as such no one could upload and it was also likely timing out.
I have rebooted the server to hopefully clear the issue, let me know if it happens again.
Windows 7 Pro, Intel i7 3.8 GHz (Passmark: 9021), 16GB DDR3, NVIDIA GTX 780 4GB Superclocked (Passmark: 8056)