Make sure you are doing the FTP transfer in binary mode. The default is ascii mode which does things like mess with (what it thinks are) end of line characters. In short, it will trash a datalog file.
You need will probibly need to dig into the FTP drivers a bit as the last ones I saw from NI controlled ASCII/Binary transfers as a side-effect of another switch setting. I'm sorry I can't be more exact but I fixed mine so long ago I don't remember the details. I just remember it was a problem.
On an ftp command level, at some point before the code initiates the transfer it has to send the command:
binary
to which the system responds that the transfer type was set to "I" (which, by the way, stands for image).
Hopes this helps...
Mike...