It turns out the problem was caused by the metadata files (._XXX.xxx that Mac OS X litters around non-HFS drives. The build system was trying to process the metadata files based on their extension (e.g. it tries to handle the metadata file ._MyClass.cpp as if it was a c++ file). Cleaning up the dot underscore files with dot_clean from a Mac fixes the problem. Ideally, it would be nice if the build system ignored dot underscore files, but this is a usable workaround.