Thanks to spacific for helping out here - much appreciated. I have indeed been away for the weekend, otherwise I would have replied immediately.
spacific is right on the money - if the Dock displays a ? then it means it can't find Yummy FTP.
I've seen a few cases of this, where people have not dragged the Yummy FTP icon to their Applications folder to install it, but have instead dragged it to the Dock and have therefore launched it directly from the mounted disk image - obviously, as soon as the computer is restarted or the disk image is unmounted, then the Dock can't find Yummy ... because it hasn't actually been installed!
Anyway, I'll email you to see how you're getting on.