Perhaps you need to dyno in a different gear in order to get close to 1:1 as possible.

 

Assuming we're talking about manual transmissions, power won't be significantly different in each gear. Using too low a gear can create a bit of "noise" because the roller/drum gets spun very quickly and it may be hard for the equipment and data recording devices to keep up. Using too high a gear can create excessive load and heat because it takes more time to accelerate through the run. The heat will obviously impact power. There may be some slight gearing losses with the deeper gears, but you're talking about a few HP.

With autos, things are a bit different due to the torque converter slippage and lock/unlock. With most stock autos, there isn't much of an issue with regards to the choice of gears, but cars with high stall TCs need to be dynoed in a higher gear.