Please insure that you downloaded FlashFXP directly from our website and not some other site, where it's possible the FlashFXP.exe has been modified.
http://www.flashfxp.com/download.php
Are you using ZoneAlarm or any other software firewall? For some reason they seem to conflict with FlashFXP. Disabling a software firewall isn't always enough and uninstalling it is required.
Are you uploading in Binary or Ascii Mode?