The Progamming Tool works only if the NAND Flash is disabled at Startup. At the original Evaluation Board this is done by removing Jumper 15 to pull down CS1. The Sparkfun board has only a pull up at CS1.
I flashed the firmware with the FT232RL Breakout Board (5V supply, 3.3V Rx/Tx) and the "flash.bat" skript from VLSI.
First check if your path variables are correct and you can compile the projekt using make clean, make all. Try to connect to the VS1000 with "vs3emu.exe" as described in the programming guide. If it works, just run "flash.bat"