I checked that, but the layers don't seem to be the issue.
I tested the original 1.0.0.4 and the raycast stops working after changing layouts.
Then I tested the exact same project with only one modification to Laser3D: resetting Laser3D_3dLayerCache when changing layouts.
That immediately fixed the problem, and Laser3D now works correctly across all my layouts.
So it seems the cached 3D layer from the previous layout is the cause.