It has to do with the inherent frictional loss of gear sets. The larger the ratio multipier, ethier up or down, the greater the frictional loss. We always dyno in 4th with a 6 speed because that gear is straight through or 1 to 1. Any other gear would produce lower numbers. Gear set frictional losses are also proportional to the torque being transmitted. The differential gear set is the major part of driveline loss. The same goes for rear gearing as dynoing in different gears only slightly effects the out come. For example going from 3.42s to 4.10s might only change things 5-6%, but the jump to 4.56s might lose you 8%. That might sound small, however 8% of 400rwhp is 32hp lost. This is all a lot of ricer math, but the theory is good.