OS Command batch script issue (FTP)

All,
I am running into a problem (i think it's simple) which I just can't seem to figure out. I have a FTP command which is in a batch script and I can run it manually (Its run in an old enviroment with Informatica) and the ftp script works just fine. When I use the OS Command to launch the bat file, it accesses the bat file but in the ftp log all I see it doing is copying the local directory into the first line of the log and then just copying the rest of the ftp script. It does nothing else!!
Does anyone have any ideas? I have copied the script and forced it into one bat file, tried running it from a local directory, running it from the server, combining everything into a single source for lcd and script, I am running out of ideas!!
- Another point is that I have to use this process as I am moving files from a server to a mainframe environment and need the ascii translate function in FTP.
Thanks,
Abhi

Update:
After some searching (and soul searching;) ) I was able to find a way to call the FTP file through an shell batch. So for instance I have a shell script that calls the FTP script. This seems to work but now the log does not create correctly (the ftp script is creating the log) it seems to copy the script from the ftp file and paste it in the log file.

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