I've just deleted the atlas and font and done it again and this time it worked. There seems to be a problem where it can get its references wrong. Also I had a 2048x2048 atlas, i deleted a load of sprites from it and it did not shrink the atlas to suit. The remaining sprites would have fit in a 512x512 but it stayed 2048 x 2048. Looks like sometimes deleting sprites doesn't recalculate the atlas.