-flatten , -alpha flatten or -alpha remove. This takes care of the reversing problem.
Unfortunately, in at least one case, it's also starts washing out my images, such that even black type becomes gray. Any ideas? Here's the last line I was using:
/home/mstucka/bin/convert a.pdf -alpha remove -gravity center -background white -resize x403 -extent 202x403 a.jpg
A straight conversion without resizing still causes the washing out. Some images process perfectly and can be composited with the faulty ones, e.g.:

Any ideas on what to try?