Inertial tests: it is common that the longer the test (higher gear) the more power that the engine can develop, this happens for two reasons:
Engine Inertia (which is unknown) causes that part of the power is used for accelerating the engine itself. For higher gears the most of the power is used to accelerate the rollers, and as the gear becomes lower the amount of power for accelerating the engine is higher. This maximum happens at first gear (in some engines it could be even about 50%), and of course at Neutral position it is 100%
If it is a turbocharged engine, the time that the turbo has for reaching its top pressure is lower in lower gears than it higher gears
Braked tests: Both issues are considerably attenuated when performing braked tests of a same duration.
Additionally, In twin roller dynos there is also another source of differences, which is the tyre deformation: normally the lower the gear the higher the pressure that the tyre does against the front roller and the higher the losses, but these losses cannot be measured in the coast down phase. Then my recommendation is using the higher gear possible in these dynos, and even increase the tyre pressure to reduce the deformation (but if you see that slippage increases then you should reach a balance)
example of tyre deformation