Let see...
I have the same issue with some code similar to your.
With this code:

1. int p = 0;
2.  
3. void setup()
4. {
5.   size(100, 100, P2D);//troublesome
6.   //size(100,100) - no problem!
7. }
8.  
9. void draw()
10. {
11.   loadPixels();
12.   while (p<width*height) pixels[p++] = color(random(255));
13.   updatePixels();
14. }
15.  
16. void keyPressed()
17. {
18.   selectOutput("Save as...", "saver");
19. }
20.  
21. void saver(File target)
22. {
23.   save(target.getAbsolutePath()+".png");
24. }

I have the same error, but the image is correctly saved.
To go closer of your code (no human intervention, one loop only):

1. int p = 0;
2. boolean b;
3.  
4. void setup()
5. {
6.   size(100, 100, P2D);//troublesome
7.   //size(100,100) - no problem!
8. }
9.  
10. void draw()
11. {
12.   println(frameCount);
13.   if (b)
14.   {
15.     selectOutput("Save as...", "saver");
16.     b = false;
17.     noLoop();
18.   }
19.   loadPixels();
20.   while (p<width*height) pixels[p++] = color(random(255));
21.   updatePixels();
22.   b = true;
23. }
24.  
25. void saver(File target)
26. {
27.   save(target.getAbsolutePath()+".png");
28.   exit();
29. }

The idea is that in your code, selectInput() is called before draw() finished, so the sketch rendering isn't done yet: it is done only when draw() is finished. Perhaps it is more important in P2D mode than in JAVA2D mode.
So I wait the drawing loop to complete before asking the user the location of the image to save.