This is the kind of thing that happens if I have a sketch that has become "unstable". I'm using Creo 4.0, and when it's going to pull these kinds of shenanigans it always tells me the sketch is unstable then asks me if I want it to "fix" the sketch. It then proceeds to trash all the dimensions and often invert a good deal of the circle (flip to showing the part I don't want).
What this fiasco has taught me is to keep my sketches really simple and use several sketches instead of one complex sketch, etc.
It sounds kind of like whatever version of Creo you are using might be doing this "automatically"? Just a guess, I've not had sections go crazy on me like this without me giving tacit permission. Unfortunately, whether I allow the sketch to be messed up or not, I'm still looking at having to redefine the geometry.
