What are your ramp test settings?
Just to be sure, are you putting the gearbox in neutral for coastdown?
If you use "costdown rate" it will force faster deceleration during coastdown. In theory you have all the power measurement settings dialed in correctly, then it won't affect the losses measurement. In practice, reasonable deceleration rates do not affect losses, and if you go for some extremely fast deceleration it will affect losses. That's especially true for roller dynos.