Have you checked (while logged in through the shell) to see if there is such a file as:
/usr/local/etc/rc.d/proftpd
?
If there isn't one, then you might want to check to see if there are any other programs at /usr/local/etc/rc.d/ and/or if FreeBSD 5.3 is using some other method for starting/stopping programs.
If the other programs that you can successfully start and stop have their file start/stop files there and proftpd isn't there, then the problem is a missing proftpd file or a file with a different name.
If the other programs don't have their start/stop files there then the problem is that DA has possibly made a mistake and used an incorrect path in their code.
Is proftpd starting properly when the server starts?
If so trace the startup scripts to see what's starting it.
Jeff