Iis – HTTP downloads slow – FTP of same file very fast – Windows 2003

I'm not too certain about how you're interpreting some things, but first off, the max speed you'll ever get from the internet here is 15 mbps, as the chain is only ever going to be as strong as it's weakest link.

There may be no proxy servers, but there will be routers between the 2 boxes, which will all give accumulated latency. Depending on the path that traffic takes from your upload machine, through the internet, to the FTP server, this could potentially be quite high. Also, if one of the intermediate routers is bandwidth throttled, this will contribute further.

A troubleshooting step here might be to try some traceroute/tracert commands from one to the other. You'll need to run a few tests to rule out transient conditions, but overall you should get a reasonably good picture of how many hops the connection requires, as well as if any of the intermediate points are inordinately slow.

Regarding your 40 mbps connection, that might not be all it seems. If it's ADSL or similar, you're going to have slower upload speeds as a consequence of the technology. Your ISP (or even one of the intermediate points) may be implementing some form of bandwidth shaping. All manner of evil could be going on.

Your NIC may also be at fault. I have found in the past that certain NICs from certain manufacturers do not behave themselves well in sustained upload scenarios, so that's another one to add to the list of things that might be going wrong.