The way these trojan alerts work are a joke for most professional/advanced users. Especially FTP users.
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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