I started everything again from scratch and it works fine again, I was copying the prefab about, considering the sizes and names are the same I assumed I could just change the spritesheet itself and it'd sort of update, but I hadn't considered the refferences.
So thats fixed now, its great.
The names can't even cause an issue if in for example, each of my 8 different sprites, all use a 10 frame 'run' animation, All named Run_001?
An interesting addition for the next 2dtk update is, if for example I have an animation relying on say my RUN frames 1-10, if I then delete the run frames, or rename them (I assume it must happen with rename too), then the animation clip can't be used, as soon as I click it it basically locks up the entire animation window, I can select another perfectly fine, but selecting the 'broken' clip breaks it, I can't even select it to click delete as it simply becomes one giant panel. This is horribly explained, but if it doesn't make sense I can take some snapshots.