I've also been having this issue. Loading a manual save is the only way I can get Rook's appearance to load correctly: if I select "Continue" when the game first loads, or if I load an autosave, 100% of the time Rook is replaced with a default appearance. It appears to be the preset I started with in the CC when I made them.
Even manual saves don't always work though. I had to reload one 3-4 times recently before it gave me the correct appearance. Going to the mirror does fix it right away, but that doesn't help if I'm not at the Lighthouse.
