Keith, when I open a new file, I only get Layer 0 and it is of course the active one. It sounds to me as if you've got a template that already contains a Layer 1 and that it is checked to be active.
Do this: Open a new SU session. Open the Layers dialog box. Make Layer 0 active. Select layer 1 (highlight its name) and click on the (-) above the layer names. Click on the black arrow that points out to the right and choose Purge Unused from the menu. Close the dialog box. Check to see what the starting template is called by looking under Window>Preferences>Templates. Close the Preferences box.
Now, using Save As... save the blank drawing in the Templates folder under its name. That's the one you saw in Preferences.
From now on you'll only have Layer 0 and by default, it'll be active.
Irony: The opposite of Wrinkly