To try and see what may be happening open up Console app in the Utilities folder. Get to the Console log window by clicking logs and choose Console.log. Hit Clear to clear the text so we have a blank window. Then try the upload. Let's see if anything interesting comes up in the Console window around the time the connection fails to try and pinpoint where in the chain the link is dropping and see if it is the computer or something else.
Try flushing the DNS cache of the computer manually. In Terminal type lookupd -flushcache and hit Return, space between d and hyphen. Restarting "should" do it too but this will be good to run after the duck drowns to see if you then can get to http://greenfrogmarket.com. If that doesn't fix it I'd look into clearing the DNS cache of your router. Some have a setting to clear it, most you just power down the router, I'd say you've tried that though.
If you are using a router, if you bypass it and connect the Mac directly via Ethernet to the modem how does it go? You may need to power cycle the modem for it to see the new connection on the Mac. Those have their caches too BTW that a power cycle will clear. If your modem is ISP supplied with a built in router and you don't use a router of your own none of that will matter.
So the same problem happens with Transmit? Not clear if it does or if it just won't connect after Cyber Duck fails.
Even if it was a temporary drop of your ISP's signal it would break the FTP connection but it shouldn't affect the other apps, thinking out loud.
Do you have another machine at the same location to try it on? I was thinking it would actually be good if you had one to put into Target Disk mode to boot your machine from to see it if is a software problem, I'm doubting hardware. Use Ethernet or you'll have to install the USB driver.
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