In order for us to fix the problem we first need to understand it. At the moment I'm not sure what's going on, However if you can provide me with a copy of the ftp session log it might help explain the problem.
Are you using ZoneAlarm Firewall? This has been known to cause problems with FlashFXP. The only solution is to uninstall it, disabling it wont help.
Provided you're not using ZoneAlarm I don't recall ever seeing this type of problem before.
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