Using "find . -type f -exec grep nodes.mat {} \;" and "find . -type f -exec grep handler.mat {} \;", it appears that the issue is within the prefabs as well:
Binary file ./Prefabs/PathNode.pfb matches
Binary file ./Prefabs/RoadNode.pfb matches
Binary file ./ExampleMaps/Roads/Roads - Road options.map matches
Binary file ./ExampleMaps/Paths/Paths - Rotation based on nodes.map matches
Binary file ./ExampleMaps/Paths/Paths - Camera freelook.map matches
Binary file ./ExampleMaps/Paths/Paths - Moving platforms.map matches
Binary file ./ExampleMaps/Paths/Paths - Rotation based on spline.map matches
Binary file ./ExampleMaps/Paths/Paths - Camera lookat.map matches
From what I am seeing, the problem is Leadwerks, on the Microsoft platform, is not case sensitive, when it comes to building prefabs and maps. However, using a hexeditor, looking at the map and prefab files, while using the Leadwerks on GNU/Linux, case sensitivity is being used.
Likely this is nothing of a solution, but an assisted investigation.