I am a novice to wheel building and the wheel that I am working on has a weird problem that I am sure has an easy answer to. when looking at the rim from the top, a pair of nipples has the spoke sticking out about 2mm and the next two has them in about 2mm and it continues all the way around. It is a bmx wheel with four crosses.

I am reading more, and I think it may have to do with the stagger on the rim. I didn't pay attention to it when I started.

I think you may have the pattern wrong.

I took a picture of the built wheel before I took it all apart and that helped me follow the pattern.

Is the wheel true now?
Do all the spokes that emerge from the outside of the flange bend behind ones that emerge from the inside?
Are the spokes on the drive side insering into eyelets towards that side of the rim?
Photos would help us diagnose.

I read some great instructions from the Barnett's Manual that a buddy has and I am going to start it all over. I learned how to divide my spokes into four sections, A,C for the right, B,D for the left of the rim, and how to find the correct placement on the flange. I will give it all a shot in the morning. I will post results. Thanks metzinger.

You have laced the flanges off by one hole relative to each other. If you would take all of the spokes out of one flange and relace them exactly the same way but one hole over, you'll be good.

It worked. Thanks for all the help. I just had to study the wheel a little more. It was very rewarding. My first wheel.

That's correct and most likely is your problem. If you look at the hub-flange from the side and you start inserting heads-out spoke, you'll notice that the hole DOESN'T line up directly across from the holes on the opposite flange. Instead it lines up in between the holes. So if that spoke you're inserting is 1/2 hole to the right of the opposite hole, you want it to go into a hole to the right of that spoke on the rim as well. Same if the spoke you're lacing is 1/2 hole to the left of the opposite hole.