First, make sure the URL for the .nmf file (NaCl manifest) is from an origin declared in your extension manifest. Before the NaCl plugin is started, Chrome searches for an extension using this origin. If no extension is found, it is considered a non-webstore app. The origin is usually the host and port, but extension manifests allow wildcards.
Second, make sure the app's installation is not corrupted by removing it and reinstalling.