It looks like a recent change altered the margins for KML plotting (frametools.py) so that now, plots created as Google Earth overlays no longer line up with topography.
In this plot, the overlay matches the topography

but here, the margins shrink the PNG file so that the plot no longer fits the topography.

Commit f0d1bf5 seems to be where the margins were changed. Restoring the previous command fixes this issue.