I have a couple of possible solutions.
First:
By chance does your PC have HyperThreading enabled?
I vaguely recall a single instance where FlashFXP was using 100% cpu during transfers (I don't recall if speed limiting was enabled) and when Hyperthreading was disabled the problem went away.
We were unable to reproduce the problem on our own hardware.
Second:
Zone Alarm has been known to mess up windows winsock and this Winsock fix below seems to solve the problem for most people. You might consider giving it a try.
Winsock Fix
http://www.snapfiles.com/get/winsockxpfix.html