I upload from VSD all the time and never have a problem. Problems come in many flavors, the most common is a bad internet connection. Even if you have a fast connection, noise or a problem 'downstream' from you can still cause an uploading problem. Simply upload again. I actually never use the re-sync option though I understand that works fine. Scott has the right idea in that if you upload several times and things still look odd, delete everything off the server and upload again.
You are getting files uploaded to your server so I'm guessing your FTP settings are correct. Make sure you check the 'Use Passive Mode' checkbox and Port 21. That works better for most servers. Off hand, who is your hosting provider? I hear Hostgator got bought out and is now having some problems for some users. Just wondering.
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