Found this, it seems to be related:
http://us.battle.net/wow/en/forum/topic/3424799129
Still digesting what it means.
Edit: It looks like they've basically invalidated the logic nUI uses for dealing with cooldowns, because the lua function nUI is hooking is sometimes bypassed by the C-code.
If I understand the above link (especially post #5), nUI will need to register for and handle the event ACTIONBAR_UPDATE_COOLDOWN, rather than hooking CooldownFrame_SetTimer.