There are a bunch of issues with paths in asset packs.
The path provided to the compiler has to be pre-normalized (i.e. lowercase with forward slashes).
The internal path from the root of the pack to the asset has to be the same as the relative path provided to the asset compiler to find the source file. In other words, you can't build an asset pack from a root other than the current directory.
OBJs can only reference MTLs in the same directory as the OBJ.
There are a bunch of issues with paths in asset packs.