The two commandlets, GatherTextFromSource and GatherTextFromAssets, use different settings for which directories files should reside in to be processed.
GatherTextFromSource uses SearchDirectoryPaths. This setting should use paths. Only the specified directories will be searched.
GatherTextFromAssets uses IncludePathFilters. This setting should use paths with a wildcard symbol in it, as it is a filter. All assets are searched, but those who pass the filter will be processed.
It appears you also used SearchDirectoryPaths in the step for GatherTextFromAssets, but it should use IncludePathFilters in that step.