I did not see Bigstar had replied to this issue before my last response was posted. He is the lead developer and creator of FlashFXP and as he can duplicate this problem he is the one who can best find a solution to it.
With speed problems such as you were experiencing the Firewall/AV is the issue in 95% of cases so it is usually a good place to start with to at least establish a baseline. Some security software has a security "feature" that some monitoring/blocking will still continue even with the software turned "off" so even when it seems unlikely its worth checking as a problem source. I am sorry that all of my suggestions in that direction appear to have been a wild-goose-chase in your specific case.
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