I dont know the answer to the scaling problem, but I just solved another problem.
I agree with the notes above that say to check your hierarchy. I have had mysterious failures, which always seemed to clear up once I got everything set in just the right order.
This morning I was trying to add a small element with IK to a pre existing Comp and I could not even get Duik to make the controller. I even tried making my own controller (no go) So I took the pieces out into their own comp just to experiment, by copying and pasting the layers. Still not working. Then I noticed that my anchor layer – the “body” had some effects animation applied later on the timeline. As soon as I deleted that, it started working.
So hope this helps someone here. If I just assume it is me doing something wrong and go looking, I find it and Duik starts working again. (Duik v13.0.2, AE CS4)