If your files change when you "FTPize"them from Unix to Windows it’s because you are transfering your files in “ascii mode”.
If you want the files to be the same on both OS, use the “binary mode”.
But why do you use the “getFile” and “bytesToString” services in order to use the FTP protocol ? 
Ftp services like WmPublic/pub.client.ftp:put only needs the filenames (locally and remotely) and you can set the “transfermode” parameter to “binary” to have the exact same file…
#Integration-Server-and-ESB#webMethods#Flow-and-Java-services