The only thing I can think of is a quest addon that isn't aware of the new quest pop up. But then again unless they are creating their own watchframe and not utilising the built in one then that would be the reason it isn't working for you I suspect.
If any of you creators of these are reading this the name of the new frame is ..
WatchFrameAutoQuestPopup1ScrollChild
WatchFrameAutoQuestPopup1
As you can guess there could possibly be more than a few there but I haven't investigated further because my quest addon works fine with it as I don't alter anything in the watchframe except the header and the minimize button.
Here's a screenshot of it working with the framestack on display. ScrollingWatchFrame is my addon and is docked in the lower right in nUI's infopanel system.
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