If you're moving a file from Linux to Windows, there's a chance that you need to modify the formatting a bit. The two operating systems use different EOL line characters. On the Linux box, trying using the unix2dos shell command on the file, which would convert the EOL line characters. The only other thing that I can think of would be to use binmode.

Some of the replies in Windows and UNIX end of line characters might help you out or better explain things.

If you're still having problems, try posting some the code and data from the file and perhaps someone might be able to shed more light on the issue.