I don't know anything about the power commander but I know how to get the FI light on!
I am currently working on a cruise control and it uses vacuum hookup, I had a vacuum leak. If it leaks enough or you unplug the switch at the end of the vacuum line (Inlet Air Pressure sensor) it will throw a FI light.
I have a PC III and I had no issues with the FI light coming on. I would double check all the electrical connections and make sure the inline plug is plugged all the way in. Next I would check to see if anything got knocked loosed, like a vacuum line as versys_guy stated above.
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