Another time it might be completely different objects that cause it, the strange thing is that it's never happened before, I played Morrowind all the way through a couple of years ago and not once did I get this issue. The only significant change since the last time is I replaced my Radeon card with a GTX 580, maybe it's some sort of shader/driver issue?
On a side note, I've noticed that Xiran's Better Music mod causes a bit of an FPS drop too, I'm thinking this is normal but I mention it just in case it's related.
I'm using MGE 3.8.2 rev 178, same as I was last time I played