I’ve just had this problem and enabling PASV didn’t help. Any other ideas? Why is this happening for a start? Is it something I had done while working on the site? The issue is only with the newest pages on the site…
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Since you say the problem is spread accross a couple of sites on a couple of machines, the general diagnostic routes tend to breakdown a bit.
I had a similar problem in that I would upload and it would start out fine, then slowly the transfer rate would drop off to a complete stall (about 50% fail rate). Aborting and retrying the upload did nothing to help the situations. I originally thought it was my host flaking-out, as I would then try to navigate to my site in FireFox after the aborted upload with similar sluggish or stalled connections.
Come to find out, my Linksys gateway was totally burping up on the FTP traffic and I just hadn’t noticed. As, I would only check my site after a failed FTP upload. In fact, I can’t say I had noticed the trouble at all during the previous several months of operation; right until the acute bout last month.
A quick firmware update rectified the trouble, and all is again well.
On the FW side of things:
“File > Publish Everything…” (Must hold down control key while selecting File menu). This should force a rebuild of all the pages and their content, to help assure that the generated file itself is complete.
Verify that the file appears complete in a browser on your local machine.
Try your upload via FW.
Server-Side (long shots here):
Can you FTP to your server account and verify the permissions for the ‘new’ files are the same as the ‘older’ files?
Perhaps this file is just being very stubborn file, and has somehow mucked up the server side of things. Logging in manually and deleting this file (so that FW will have a clean slate) may be exactly what is needed.
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It appear that the problem in the end was the ftp space had exceeded its quota. Someone else had been uploading stuff and filled it up. Lots of cool tips in your reply though - thanks! 
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