Since the most recent August 2016 update, Illustrator and indesign no longer save preferences along with plenty of other bugs.
indesign - default opens documents in High quality which is a stupid idea if you are a designer with large files (even on a high spec iMac), after changing this numerous times in the preferences panel it does not save and goes back to this annoying setting each time.
Illustrator - same thing, units is px as default, once changed in preferences it reverts back each time you open the programme. Also the dimension boxes (X,Y,W,H) at the top when you click on any object always display in px regardless of preference change. Im unsure whether the preferences actually change anything at all?
This is a known issue. I think it's being worked on, but in the meantime, I found advise on other threads that worked for me after a few false starts (InDesign crashed the first time I tried this, but it worked the next time).
With no documents open, set your display preferences to Fast, then quit. Open a document to confirm that the Fast setting has stayed. Close that document, move the setting from Fast to Typical with none open, then quit InDesign again.
I was able to get mine to hold onto Typical by following the steps above. It's a lot of trouble, but maybe worth it - The High Quality display was really slowing my documents down, and I was having to change it every time I opened one again.