Am having an strange issue in which DO has some sort of a problem at the very end of a filetransfer. The file in question (~6.5GB) will momentarily pause when it really should be finished, and then start the transfer all over again.
The FTP log tells me that the pause = "Timeout on Command 1018".
The remote server reports itself as: ProFTPD 1.3.1rc2 Server (ProFTPD Default Installation).
Am actually downloading from that server, not sending to it.
Just finished the same file using CuteFTP. Apart from 2 unexplainable timeouts that did not seem to correct themselves (probably due to me not setting it up properly), the file transferred correctly.
First thing I'd look at is anti-virus stuff. If you're running an A/V or firewall tool that can scan data as it arrives via sockets, it might have a "compatibility" slider that you can adjust for different apps.
As an example, NOD32 (which I use) seems to buffer up all the data that Firefox downloads, and once a large archive is completely downloaded it blocks the app (Firefox) from seeing those final pieces of data while it scans the archive in its buffer. On a big archive that can take so long that Firefox decides the network has timed out and aborts the transfer. (Yet using the DownThemAll extension within Firefox works fine.) NOD32 has some compatibility options, though I've not played with them (I got used to using DTA for large files).
The delay/timeout could also be caused by the app writing the last bit of the file to disk and triggering a real-time disk anti-virus scan, though in this case that seems less likely since the file would still be fully downloaded. (Still possible, though.)
Interestingly, I also use NOD32 and was myself suffering from the "large download" issues the you mention, but that's worthy of an entire topic on it's own - just not on this forum.
Will retry the download with NOD32 switched off completely and see if that helps, I have a strong feeling you are onto something.