This is how I usually flash the thing:

- turn off device, pull battery, connect cables
sudo ./flasher-3.5 -F [Fiasco image] -f

- put battery back and pull it out after the flashing finishes

sudo ./flasher-3.5 -F [eMMC image] -f

- put the battery back
- after flashing finishes reboot the device

Works for me 100%