You are trying to do the one thing Creo, Wildfire, and Pro|E are simply not equipped to handle. Better to simple pattern the sketch about an axis than to associate it to a different CSYS.
I didn't read all of the text above, but the bottom line is that things flip way to easily in Creo. It is a problem in every respect with no simple solutions. This happens in sections; patterns; and assembly constraints. Something PTC has never sought to enhance.