I have created a saved setup with the correct layout and settings, and that is the only one in my .dwt file that is mapped to my SSM for the "Plot with page settings overrides.
But - in the sheets, there are about 4 or 5 saved plot settings (full pdf, half pdf, full plotter, half printer, etc) and if one of these is active - the "Publish to PDF" from SSM uses that setting. That was what I was running into.