Blame it on teh MS box. MS's TCP/IP stack is horrid, especially if it's pre-2k. From 2k on, they started using more and more BSD code for their TCP?IP stack, but I"ve timed transfers from one box that dual boots, linux and windows. The file transfer from linux is usually 2x as fast as from windows.
I've no idea what was going on, I could ftp with ease from one NT box, another NT was slow as hell, a 2k box was the slow one I was refering to but half way through the day it started getting much speedier. There was no change in network conditions.
Must have been gremlins.
It's working better now, so my boss is happy, which was the aim.