Only happens to my account. I tried a test account and it seems not affected.
After I changed my preferences and submitted the form, it appears to be successful, and new preferences are shown in the returned form, but it seems not saved to the database, that is, behaviors of the site are not changed, and when I open a new Special:Preferences page, old preferences data are shown.
Version: wmf-deployment
Severity: normal
Hmm sometimes it works but sometimes it doesn't.
After some experiments by watching https://zh.wikipedia.org/w/api.php?action=query&meta=userinfo&uiprop=options&format=jsonfm , it seems that at least in some cases, new prefs are saved, but they get reverted soon... Weird.
(In reply to Kunal Mehta (Legoktm) from comment #4)
Are they random preferences or specific ones?
random preferences
I encountered something similar at fiwiki today (only looking at the web UI with Firefox, not API), but reloading the page apparently cleared some cache or something like that, and everything appeared as it should. @liangent, could that be some (client-side) caching issue for you as well?
Closing this ticket due to the age of the ticket and lack of steps to reproduce. If this problem is still occurring, please feel free to reopen this ticket with updated steps to reproduce.