If they were fatter they would set up on your rest higher, making them shoot higher. If your carbons are thinner they will set lower and point down more, making them shoot lower. I don't know if that is it but it was with mine. I was shooting 2312's for 3d and when I switched to carbons they shot lower.
Have you shot them through a chrono and paper tuned it yet with the carbons?
You will be able to see the speed difference with the chrono and you may need to retune it because of the different diameter, spine difference, and weight.
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