You can try the following
When you FTP the file to the service, specify the content-type as "application/x-wmflatfile ". This should definitely bring in the *ffdata stream object inside your service.
Or if you know the extension of your file (like *.txt, *.dat) is fixed, you can add it to the file \IntegrationServer\lib\mime.types.
Btw, please make sure your WmFlatFile package is loaded as a startup service initialises the content handler for "application/x-wmflatfile ".
p.s. The pipeline will be empty until you specify the right parameters for the content handler to provide the correct stream object. So it doesnt help to try debugging with savePipeline service.