I am not sure if that's similar case to the OP's case, but on
4PDA there was a discussion about Bookerly. After 5.13.2 Amazon changed the hinting mechanism of the fonts to autohint, leaving the hinting to reader, while they stripped the fonts out of their native hinting instructions.
You could probably find the old Bookerly font and try use it as external one to see if this will fix it, or problem is with the new hinting mechanism.