Wow I am in the exact same situation. Our district uses the CogAT as well. My son scored about average on that specific test. He also scored 99.8 percentile on the WIAT in math and is currently in EPGY (Stanford) and just qualified for CTY (Johns Hopkins). In their above level test he scored in the 86th percentile when compared to children two grade levels above. He doesn't qualify for GATE, however. Almost everyone we know is in the GATE program except my son.
I gave up trying to deal with them and I used EPGY to keep my son interested in math. He is exceptionally ahead of his classmates in math yet he is in gen ed.
He is also autistic. This may be why he did poorly in the group CogAT testing. Still they did not retest him or take that into consideration.
So you are not alone. Try using some outside gifted resources like EPGY
http://epgy.stanford.edu/or CTY
http://cty.jhu.edu/Good luck! I think that there are many like us.
