OK, I figured it out. This is maddening, but at least I know what's going on. It turns out it was layers after all.
In the part I've got our default, rule based layers. I had the "00_NOTE" layer isolated to see an onscreen annotation. If that layer state is unhidden or isolated, when I create my drawing, a "00_NOTE" layer is created at the drawing level and all drawing notes are placed on it and it's display is set to unhidden.
Since an isolated layer effectively turns all other layers to hidden, my notes disappear!
If it's set to unhidden, the layer is created, but the layer statuses do not conflict, so all appears to be OK.
I tested setting all of my default, rule based set to isolated and the only drawing layer that gets created is the "00_NOTE" layer. I also tested it without the template, and the drawing layer is not created, regardless of part layer status. I checked the template layers again and there are none. Something about the interaction between the template and the rules in my layer is generating this behavior.
Crazy and unexplainable, but at least easily repairable now that I know what's happening. Jus delete the drawing layer.
I haven't checked the behavior in WF5 or Creo X.0, I need to get back to productive work. 😛