Your right, I haven't been able to figure it out and since I can't reproduce the problem on any of my machines it makes this very difficult to solve.
Some people have reported that FlashFXP v2.x doesn't have this problem but the underlaying transport routines for v3.x are almost identical and the changes that were made do not appear to be causing this problem.
UPNP would effect incoming connections (PORT) and you are experiencing this problem with outgoing connections (PASV).
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