If you search the forums you'll see several posts similar to yours, results seem to varry from system to system. FlashFXP may perform very well on one system and while just average on another.
If performance is your desire over cpu usage you can change the FlashFXP.exe priority from normal to high. This can be done via windows task manager or you can do it via the FlashFXP.ini
open FlashFXP.ini in notepad
add "HPC=1" under "[main]"
such as
[main]
HPC=1
save FlashFXP.ini and then start FlashFXP
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