np
If it's of any interest of you now there's a couple other ways to do this as well. Sadly I'm not entirely sure which build these were added in.
The registry key
[HKEY_CURRENT_USER\SOFTWARE\FlashFXP]
"DATAPATH"="C:\PATH\TO\DATA\FILES\"
Via the command line
FlashFXP.exe -path="C:\PATH\TO\DATA\FILES\"