I downloaded the latest full package for Joomla to test this out for myself.
System Environment
* FlashFXP v3.4 build 1145
* WinXP SP2
* 1024/768 DSL
* Local network is gigabit, a gigabit switch connected to the dsl modem.
* ProFTPD (not sure what version off hand)
* NOD32 Anti-Virus
The connection and data transfers utilized SSL/TLSv1 encryption. I might of had slightly better results if I didn't use encryption.
Transferred 1,551 files totaling 6.41 MB in 21 minutes 12 seconds (19.7 KB/s)
Due to the large number of small files the performance is limited by how quickly the client/server can send commands back and forth as well as open data connections.
One possiblity is that your firewall limits the number of connections per second which would increase the overall duration of the transfer. However this might not explain why WS_FTP managed better results. Another possiblity is that perhaps FlashFXP needs to be optimized for your network setup. Basically this means adjusting the TCP/IP Buffer Size option within FlashFXP
Options > Preferences > Connection > TCP/IP Buffer Size
My first suggestion would be to try (default), and then work your way up from there.
When changing this setting special care must be taken, It can only be changed while disconnected from all sites. If you are connected to a site the change wont take effect until you restart FlashFXP.
(For my test I used a 32k send buffer, this seems to work best for my network setup)
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