Ok, I no longer think this has anything to do with the touch layer.
What i did
1) made an all black img and put in on my iPhone
2) looked at the image in Photos app.
3) tapped to turn on the photo controls
4) tapped to turn off photo controls
5) dragged slowly in from the right
6) dragged slowly in from the left
7) switched back to home screen
What i Observed
When i looked at the dots on a all black screen the dots where spaced out and checkered.
When the photo controls where on the dots where tighter together and in line.
When i drag a photo in from the right (the next photo in the album, so i pull my finger left) the dots remain checkered.
Now the fun part: When i pull the photo in from the left (prev photo, drag my finger to the right) the dots become tighter in pattern on an angle (about 45 deg) down to the lower right. As i dragged further to the right the dots moved along with the top left corner of the prev image. further filling the screen.
then when i switched back to Home. they fill the screen with the tight pattern except at the top.
My conclusion (this is so much fun, like cem lab back in High School)
The dots appear on the LCD it itself, they appear tighter to the right and descend down from any on screen pixel. this is also why at startup, the tighter dots are only on the lower right of the screen, because of the big apple logo in the middle. also why the tight dots are not at the top of the home screen where there is no text.
I sill don't know what they are, or why. bit the fact that they only show half way through start up and def react to pixels on the screen leeds me to believe this might be fixed with software.
Here are my images. sorry about my hand, but I'm holding the photo. i adjusted the exposer to enhance the dots.