The Encore project is set by what you select in the "NEW PROJECT" menu when you create a new project, it will ask you then what standard you want your project to be created in.
The settings PAL / NTSC in the preference menu are for display purposes only.
Thanks for solving the mystery! I appreciate the explanation of why setting the preference menu has no effect on the actual video standard. One wonders: wouldn't it have been nice for Adobe to explain that in the Preferences? Or did I miss that too?