I am doing nearly the same job like you: Scanning with DAVID and using the B9C Slicer to provide my self-built DLP printer with the necessary slices.
Yes, you are right, both coordinate systems don't correspond completely. Therefore I use the free MeshLab software to turn the scanned object in the right position for Mike's layout build platform.
Import the Mesh file as OBJ or STL.
Goto Filters (top left) => Normals, Curvatures and Orientation => Transform: Rotate.
Choose for center of rotation: barycenter.
Don't rotate the object by mouse, its position isn't absolute!
Export as STL.
Fine rotation in the B9C layout window.
PS. Here you can find DAVID's coordinate system (Jul 22th):viewtopic.php?f=10&t=4699&p=23362&hilit