I kind of gave up on Keynote Extractor, but since Apple released a new version of Keynote I tried to use it with Keynote Extractor 1.1.
After some testing I verified it works fine with the newest version of Keynote (8.1).
I haven’t run into the “jumbled slides” bug anymore. I figure maybe something was changed on Apple’s end making it so that the bug doesn’t happen anymore. Yay!