I'm not sure why FTP v6 would be slower, and I'm also not sure what to else to have you try. I compared uploading with Photo Mechanic to our test server compared to uploading with Cyberduck and got roughly similar speeds. I also set up a simple FTP server on my personal laptop and uploaded to it over my home wifi network, and got similar speeds between the two pieces of software there as well, but then again, my uploads were going at about 10 MB/sec. Not even remotely close to what you were seeing, maybe I'd be seeing a bigger discrepancy if my network was capable of faster speeds overall.