The same thing happened to me and this is what I did to fix it:
1. Plug in/power up the MF while holding down the 4 corner buttons to enter DFU mode. You should still either get just the corner light or all lights lit up. This doesn't matter (at least it didn't for me).
2. Follow the "1. PC using Atmel Flip" instructions from here to flash the firmware on a PC.
3. IIRC, after the flash is complete, 3 of the lights on the top row (C3, C#3, D3) will blink 3 times sort of slowly. You must wait for these lights to flash for the firmware to flash properly.
4. After you see the lights flash, disconnect and reconnect the MIDI Fighter.
This is the process that worked for me after hosing my firmware initially. Hopefully it works for you, too.
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