So, this was the solution for me and problem I was seeing...
Solution:
[[CCDirector sharedDirector] setDepthTest:NO];
(changing setProjection was not necessary for me, as was suggested above - luckily because that would not have worked with my project)
This was the only thing I had to change (setDepthTest) to remove the flickering.
This of course broke the transitions I had going on between pages so setting
[[CCDirector sharedDirector] setDepthTest:YES];
just before doing a transition and then setting
[[CCDirector sharedDirector] setDepthTest:NO];
after transition was done fixed that problem.
I was seeing the problem with translation animations on large images/content that was moving from outside the screen area into the scene (or vice versa), might be different for others but basically if I understand the original posters problem, flicker occured when he was scrolling (somehing that's outside the screen into it, larger than the iPad window, thus the need for scrolling)... So there was flicker...
For me flicker occured when a certain percentage of the image/content was outside moving ino the screen (or the other way around) and in those places where the image/content was.
Changing setDepthTest removed the flickering and didn't break anything on the original iPad (but as noted above, I had to change the setDepthTest back during transitions to avoid funkiness in transitions).
Probably common knowledge by now - but I had and solved this problem a couple of days ago and thought I might share what I found if it helps in any way...
