Jynx was supposed to represent a type of makeup used in traditional Japanese theater and among the "ganguro" people. (I have no idea how it came about, but the ganguro are these eccentric Japanese girls and women who dress like clowns. They wear neon wigs and brightly-colored clothing with tons of makeup on their faces and often a tan. And they're covered in glitter. It's a major turn-on for some boys and is a kind of 1980s fashion gone horribly wrong.)
What happened was that African-Americans...well, only a few of them...interpreted Jynx as an actor in blackface, a kind of make-up for whites to look black in old movies, like Gone with the Wind and Birth of a Nation. Like normal Americans, they protested, complained, and theatened to sue, so Nintendo made Jynx's face purple, and they were okay. That is, until the California Raisins are genetically engineered and get cranky...