First of all, sorry for the trouble. In future situations like this, I would recommend contacting me by email since this will get to me quicker and I can help you sooner.
The issue is known and is a bug in 1.9.3 with Dropbox sync. The Dropbox -> Yummy FTP folder
must be on your main hard drive. This is fixed in 1.9.4, coming as soon as I can finish it… I'm working flat out to do that right now

For the other few users with this issue, they simply have their Dropbox folder on another HD, so it's simple to fix, but in your case, since the whole Users folder has been moved, so I'm afraid you'll need to move it back for now. You could also try going back to 1.9.2 temporarily:
http://www.yummysoftware.com/archive/Yummy%20FTP/1.9.2/YummyFTP.dmgLet me know if you need more help.