As the title says, I'm getting tons of extra copies of this book because I rarely have a pearl on hand when I activate my pearl farms. Annoying, but minor.
NEI issues I'm having, are another story, but likely my fault somehow anyway.

Yeah, it's a known mistake. I'm checking the wrong tag each time. Will be fixed next version. It also happens with the factory, fishing and diving books but you don't notice it as much as they you don't perform that action as often. Not sure when that update will be, as I'm currently focusing on 1.7

Should be fixed in 1.2.1.