Is FlashFXP using Passive Mode (PASV) Or Active Mode (PORT)? You can tell by loooking at the ftp session status window.
I suspect CuteFTP is using PASV mode and FlashFXP is using PORT mode.
You can enable PASV mode in FlashFXP Options / Preferences / Connection Tab.
These false alarms are caused becaused FlashFXP is using the same ports as known worms by NAV.
FTP uses random local ports when using PORT mode, One solution you can try is to limit the local port range in the Preferences / Connection Tab.
I'm not sure which range of ports are blocked and which are not, but you could try a port range of say 11310 to 12310.. This is just a random range I came up with, feel free to try another range. If the range of ports is too small you'll run into problems, usually 10-20 ports per copy of FlashFXP is a good measure.
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