I'm transferring a large file, and it keeps going from 10mb a second, down to just 200-300kbps. I've read up on your site that changing the cipher from AES to Blowfish should help. It did indeed. The problem is, the setting doesn't seem to keep saved :/
I made sure I pressed "save" when leaving the settings - I then closed WinSCP - reopened it and the setting has reverted back to AES.
Is this a known issue?