I am also having the same issues. I've noted that the extreme drop in FPS happens whenever an objective gets partially/fully completed causing the kill/collection counter to go up.
For instance, Stormwinds fishing daily, I will fish fine, but when I catch the walleye, as soon as the counter pops up, ex. "Walleye 2/8", that's when it chugs to a halt until the text fades away. Or for the Valentines quest, analyzing the guards' perfume, every sample taken, as soon as the text pops up, chugs to a halt. Every time, not just sometimes.
I disable Carbonite, and the issue goes away.
I hope I was thorough enough in my explanation
