Out of curiosity which specific builds did you test?
When you installed v3.0 did you install it into a new folder?
It is possible that a legacy setting left over from v2.x is slowing it down. To eliminate this possbility you will need to delete the FlashFXP.ini, this will clear all your custom FlashFXP settings.
Results seem to vary quite a bit from system to system.
On my systems v3.0.2 is much faster than v2.1 hands down.
Most of the transfer code was not touched in v3.x
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