I developed a basic WF to add some file_metadata read by an eml filter starting with version 4.7.1 of Mayan-Edms. Everything works OK when I load eml files through the web interface. However, when I import the same files using the Watch folder, Mayan-edms recognizes them as plain text files rather than mail messages.
EML files are a container that includes one of more files. They behave like ZIP files. If you upload the EML without decompressing it Mayan will detect it as an EML file. If you decompress the EML during upload (GUI or sources), the files contained by the EML will be detected as their corresponding MIME type.
In your case it seems the upload via GUI and via sources are configured differently when it comes to the decompression setting.