Super Hamster: I can't explain it, if I could it would make my life much easier.
I'm not saying v4.1 is perfect, clearly some users have seen a decrease in transfer speeds.
What TCP/IP buffer sizes are you using in 4.1 and in 3.6? Have you tried different sizes? If not I would suggest you do that. When changing the TCP/IP buffer size you need to be disconnected from the FTP server for the change to take effect.
Also make sure that you have MODE Z compression turned off in FlashFXP.
In addition it would be helpful to know specifically what FTP server you're using to test against, not all FTP servers are created equally and some perform better than others under certain conditions.
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