Hey guys, apologies for not checking on this post for so long, I really appreciated the help I got trying to isolate this problem.
I ended up buying a new Di2 RD ASAP and replacing it. my Di2 on my road and TT bike has worked flawlessley aside from this problem which I think could have been caused by the crash. I think it may have just been bad luck when it did start malfunctioning 6 months after the crash, I have no way of telling how close it was to failing before this, maybe it was just a particular bike washing episode that allowed water in through a crack or damaged spot that had until then luckily avoided it
It was expensive and I'll admit to being lazy when it comes to sending stuff in for warrenty work, but I ride my bike every day, and get most things (Shimano included) at trade price through a friend.
I don't know how common these problems are with Di2, I really enjoy using Di2 so this hasn't put me off.
In it's defence although the RD only had scuffs to it and I was able to ride an home without any adjustments to the RD I have no idea how hard it hit the road. I needed 18 stitches in my hip from the crash so it did better than me