Thanks for the help Chris.
That isn't the issue, I was selecting the character and the red box was appearing.
As it turns out, for whatever reason, CTA2 was adding a keyframe whenever I added a new character. It seems to add a keyframe every time, no matter what character I was adding. What I found was that the presence of this keyframe (I think it shows when I select transform / flip) for a given character is the transform / rotate etc actions for the character at the start frame don't work. I found that by deleting the keyframe, then I was able to transform the character at the start.
Anyway, hopefully someone can verify this or clarify. Anyway, I delete the keyframe every time I create a character and then all is well and I can reposition the character.
I think I gave up on CTA1 because I couldn't figure this out