Underhand involves the Teres Major to a greater degree and definitely the bicep more than overhand or wide grip. Underhand lat pulldowns are a staple in my back routine. I like the vertical stretch it gives me and I can really contract hard on it.
When you say "cracking" I think of bone... is it more like a snapping sound? like a tendon maybe? Like Reinheart says, make sure you are thoroughly warmed up before your working sets. But sometimes certain people just can't do certain exercises... Like I get a cracking and popping whenever I do upright rows w/ a barbell...