Is there any way to do a manual upload via cute FTP?

Yes, either use that or CoffeeCup Direct FTP, free version. Here's a note, on your FTP settings please make sure you are doing a BINARY upload. For some reason it does make a difference sometimes. At least on my sites.

Hiya Chuck,

Before you do the manual upload method I really would suggest putting in a support ticket to CC team to see if they can help you sort out what may be wrong. Does sound to me like settings aren't correct as Eric has suggested and CC can most likely help you sort that out. You can always do the manual method if they can't help with it, but using VSD's internal uploader is much better for the program to be able to sync and such later.