If there is no code, that's not a Programming Question, but a General Discussion topic... I will move it unless you show how to reproduce your problem. BTW, I see no "boxes" in the image you posted (too dark?).

PhiLho, the black boxes are seen in the places where butterflies are too near each other, you can see how some butterflies are covered in black because of the butterflies above them.

billautom, try making the flapping effect using the scale() function instead of rotateY(). You should try something like scale(0.9 + 0.2*sin(millis()*0.01), 1);

Here I wrote a little program which draws 10 butterflies on the screen and makes them flap. I used noise() function to generate their position and I added the "+i" in the sin() function to offset their flapping (without that they would be synchronised which looks unnatural).

1. PImage img;
2. float xx, yy;
3. void setup() {
4.   img = loadImage("http://www.fordesigner.com/imguploads/Image/cjbc/zcool/png20080526/1211766518.png");
5.   size(1280, 720);
6.   imageMode(CENTER);
7. }
8. void draw() {
9.   background(0);
10.   for (int i=0; i<10; i++) {
11.     xx = width*noise(i);
12.     yy = height*noise(i + 10);
13.     pushMatrix();
14.     translate(xx, yy);
15.     scale(0.9 + 0.1*sin(millis()*0.01 + i), 1);
16.     image(img, 0, 0);
17.     popMatrix();
18.   }
19. }

1. PImage img;
   void setup(){  
     size(1024,768, OPENGL);
     img = loadImage("1236.png");
     img.resize(floor(img.width*0.3), floor(img.height*0.3));
     imageMode(CENTER);  
   }
   void draw(){ 
   }
   
   
   void keyPressed(){
     if(key == 's'){
       saveFrame("#######.BMP");
     }
   }
   
   
   void mouseMoved(){
     background(255,0,0);
     for(int i = 0; i < 128; i++){
       pushMatrix();
         translate(random(width), random(height), 0.0);
         //rotateY(random(-HALF_PI*0.2,HALF_PI*0.2));
         rotateY(frameCount*0.01);
         image(img,0,0);
       popMatrix();
     }  
   }

When I created the equivalent openFrameworks application I had to call the ofEnableAlphaBlending() method in order for my transparent ofImages to be drawn correctly.

I am not a specialist of OpenGL but I saw several messages mentioning issues with transparency in this mode. A quick search of the forum shows lot of threads... Perhaps one of them has a solution.