I think Stephen is maybe talking about Ignore CR and Ignore LF? That is for handling parsing issues of the DOS pair CR/LF (hex 0D/0A), which is two chars instead of just one.
If I understand correctly it sounds like there are two CR/LF at the end of your flat file? Try creating an outer record around your file that can absorb the extra CRLF.
Otherwise explain the issue again if I have not understood it. I just made some FF schemas recently, so I have the info fresh in my mind.
- weak architect