Color blocks and lines im Photo

I just got Aperture 3. When I look at my pictures for just a few seconds they are clear then different color blocks appear in the picture. They are not present in the thumbnails only when I open a picture. Also I can open the same photos in iPhotos with no problem. If I have both iPhoto and Aperture open it does it in both programs. Apple replaced the mother board on my MacBook Pro and they say this is not a hardware problem. I'm not so sure.
Does anyone know how to fix this.
Thanks.

craigganojm
When I have Aperture open it appears to affect my whole system, I’m wondering if it is the same on your system? I have checked activity monitor and am not using all my RAM although I appear to be using most of it. I am going to try a clean install and see if this helps.

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May be it has already discussed in many forums but somehow I got confused about different solutions of the questions and due to this asking once again here.
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