Are you making full frame prints or are you cropping to enlarge a small area of the negative? Even a large format negative can look grainy if you "zoom in" enough.
Yes, you will see grain suddenly "pop up" when you look through the focusing magnifier. That's what's supposed to happen. It tells you that you have the image in focus. However, the final print shouldn't show too much grain unless you look closely.
Also, don't forget, you can see grain in many prints, even well done prints, if you analyze from a close distance. Normal viewing distance for an average size print is usually considered to be approximately arm's length or more.