It's possible that the TCP/IP buffer size set in FlashFXP isn't optimal and this can degrade performance.. You can adjust this via Options > Preferences > Connection > TCP/IP buffer size.
I would recommend trying "(default)" first if it's not already set and then moving on to other values to see what work best for you.
(You must not be connected to any ftp sites when you change this setting, otherwise it wont take effect until you restart FlashFXP).
Also switching between Active mode and Passive mode can sometimes improve performance. This can be set either per-site or globally, look for the option "Use Passive Mode".
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