You shouldn't have any speed problems with downloading, FlashFXP can receieve as fast as your connection can handle.
Uploading on the other hand was not very optimized using 1.4.2 (build 631) or below, Just recently we have optimized it and you need the latest public beta to take full advantage of it. You can download it from the Public beta forum.
Using the latest public beta I get the following results on my 100Mbit LAN w/ MS IIS 5 FTP
Upload
Transferred: access-flashfxp.log 25,353,587 bytes in 3.13 (7,897.72 KB/Sec)
Download
Transferred: access-flashfxp.log 25,353,587 bytes in 3.74 (9,023.09 KB/Sec)
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