Scoring meshes vs MultiFunctionalDetector scoring


I’m running a code firing a photon beam at 2D water phantom (50x50x1cm), I have two implementations with identical input parameters for their geometries and separations. In the first instance I have used a macro file scoring mesh with water at the position of the scoring mesh, and received values of incident particle fluence. In the second instance, I have created a multifunctional detector water phantom (basically RE02), and am reading out fluence from Registered primitives. My fluence results are ~10x different with each of the methods. Are there any differences that I should be aware of between these two scoring styles and is there a preferred option given the limitations of each?

Many thanks.

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