As a postscript, after regenerating all the elevation data and
spending all that time trying to figure it out... turns out the
problem had nothing to do with elevation data! Was just a stupid bug
in the code that outputs final user-viewable route from the shortest
path points. See http://code.google.com/p/sf-bike-planner/source/detail?r=40
Ah well, at least it spurred some improvements in the process.
p.s. I am now a proud father! isabella is 3 days old