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.