That seems rather odd. GatherTextFromAssets doesn’t actually iterate over directories. It looks at packages and, if their file path matches an IncludePath, adds them to a list of packages to be loaded for later processing. As such, any packages existing in subdirectories should be accepted by merit of matching the include path wildcard for the parent directory.
Out of curiosity, is it possible that these assets have been relocated and have redirectors that need fixing up? If so, this might reveal an issue with gather text from assets that have been relocated and have outstanding redirectors in place.