You mean the beta version? Which specific build?
FlashFXP will use all free cpu cycles to transfer the file as fast as possible. However on my 400mbit firewire pc to pc connection I can transfer at max speed using a ram disk and the cpu usage is far from 100% closer to 30%
If you're uploading check your upload packet size (options / preferences / advanced tab) if this size is too big or too small it will use more cpu usage. 4096 or 8192 seem to work best for most people.
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