I have exactly the same problem when FTPing from PC to Xbox using Flashfxp 2.0
For some unknown reason I go into the main C drive on the xbox and can only see a handful of files. The first time I noticed this I shit myself because I couldnt see my config.xml file. Without this the xbox wouldnt even boot, so of course I copied over a previously backed up copy of the file I tought was missing and was told by flashfxp that the file was already there and would I like to overwrite it, I said no, went with god and rebooted the xbox.........................and it worked fine.
I have had a good search through the forums and couldnt really find another error the same until recently.....so had to do a few things for myself to see if I could resolve it.
Someone mentioned that it might be because I was using an old or error ridden version of Flashfxp, so I download a trial version and still the same problem.
So I thought I wouild trya simlpe but backwards way of FTPing the xbox. I went in via Internet Explorer.........and low and behold I could see all of the file. There they all were in all of there glory (making me happy that I was not going mad).
Now whilst I could really continue to use IE, I would really lilke to be able to use an FTP package directly...
Someone mentioned that it is down tro filezilla, and tat it is a problem that has been about for a bit, another idea was that it could just be FlashFXP...(can't confirm that as I havent tried any other ftp clients yet).
So guys, I leave it down to you. If you have any better ideas please let me know.
Jon