For those with save transfer issues...
Now I know that I shouldn't keep posting discussions like this but I have contacted Telltale with my info here so they can help everyone get this sorted with an official post, but until then I'd like to give people a fix. While talking to Telltale they told me to check through my choices for Season 2 and lo and behold one of mine was corrupted (Basically on the "My Choices" screen at the end there were only 4 choices listed instead of five) because it turned out a choice of mine in Episode 2 hadn't counted.
I replayed through all of Season 2 from the end of Episode 2 and my save now works and so i will be replaying S3 Ep. 1 and 2 to have my REAL save data. Thanks Telltale for helping me with something that seems rather obvious now.
P.S. If anyone else has made a post like this, or said something like this, then I'm sorry but I was too excited to check by the first page.