Have you had a chance to look at the exact type of questions that were used for each subtest? I am not terribly familiar with the CogAT because only one of my kids has taken it once... and it was through the school district so they didn't share a ton of info on it. I found that with my kids' WISC-etc tests there were often score variations that I didn't understand just on the surface based on what I knew of my kids strengths and weaknesses, but when you dug into the details of what each subtest asked, how it was administered (oral vs reading) or how replies were made (circle, writing, oral response etc) the variations actually made sense in the context of the individual child.
Best wishes,
polarbear