Keep in mind that when you're in a crowded area, that actually has nothing to do with nUI at all because it only interacts with units that are in your group/raid/target -- I have seen this phenomena myself since the 3.0 patch to WoW and I know it has something to do with the graphics engine.
It is only a theory, but I think having an intense mod such as nUI magnifies the problem by adding CPU load to a system that's at the breaking point as it is. Make no mistake, nUI is replacing darn near the entire UI, so it has a penalty for use no matter how you slice it... add that on top of a graphics engine on the verge of collapse due to all of the elements it has to render in a busy area and suddenly your frame rate craters.
I also firmly believe Bliz flat out broke add-ons with the 3.0 patch and given the new add-on development guidelines, I'm less confident they intend to fix it. Clearly, as of the 3.0 WoW patch add-on performace dropped dramatically and there's an unmistakable penalty of having add-on memory usage at or near the 100 meg mark now.
Tie all those things together and even a hot gaming PC is going to see issues unless all of the stars and planets line up just so.
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