This happened to me. I had put an folder in the E: partition and the next day, the folder wasn't even there anymore! The weird thing was I could still access the folder if I typed it in manually! I just couldn't see it on the screen. I hit refresh and tried clearing the cache to no avail. I was using smartftp. So I decided to give flashfxp a shot again, and it worked! I can see all my folders now. Damnit! I liked smartftp so much more but I had to switch. Maybe you should try a different ftp client.
iMURDERER