I've been stuck on this FTP issue for a while now. I have IIS 7 setup with an IIS 6 FTP server running on a Windows Server 2008 box. The problem I am running into is that I can't download certain files from the FTP server, even though I uploaded those files to the FTP server. The connection times out after 120 seconds. I have used Wireshark and checked the log files. The only message I see is the timeout message. The first thing that came to my mind was permission issues, however I have probably tried every combination of permissions that I can think of, with the end goal of getting the permissions to be the same for the files that work and the files that do not work. With the list of files I have now, I can download the zip, war, and msi files, but not the txt or sql files. It almost seems like a binary thing, but I've changed my transfer mode on the FTP client and also toggled the Active/Passive options around.
SnapOverflow
Another troubleshooting step would be to temporarily disable real-time AV on the server and/or the client. Have you tried different FTP clients?
Check if those files are not in use. You can use Process Explorer for that (Find handle or dll...).