Guaranteed Transmission Protocols For Windows?

Michael writes "Part of our business at my work involves transferring mission critical files across a 2 mbit microwave connection, into a government-run telecommunications center with a very dodgy internal network and then finally to our own server inside the center. The computers at both ends run Windows. What sort of protocols or tools are available to me that will guarantee to get the data transferred across better than a straight Windows file system copy? Since before I started working here, they've been using FTP to upload the files, but many times the copied files are a few kilobytes smaller than the originals."

Comments

TCP?

[causality]

The summary states that with FTP, the downloaded files were of the wrong size. Can anyone explain why TCP's efforts to to deal with unreliable networks, such as the retransmission of unacknowledged packets and their reassembly in proper order, would not already deal with this? I am familiar with the concepts involved but I think I lack the low-level understanding of how you would get the kind of results the story is reporting.