Yes, I see what you are saying.
What kind of FTP server are you talking to?
The next step I would suggest is to leave the last proc in send ok.
Create a new eo alias for fset/control/debug/1 only.
Enable that eo alias and see what response you are getting for each missing message from that server.
One last thing, the file that you are looking at from the other host;
is that a virgin file or has it been processed by some program by the time you look at it?
-mh