[Piotrsko]

Based on what I observe over on some of the other power forums I stalk, you have probably fried the power transistors and probably also the drivers.

Isn't there some snubber diode across the igbt to sink the back emf?

From what I recall igbt failure mode is generally shorted on. Theory says the gate becomes damaged.

My experience is that it doesn't take long to crispy the weakest part reverse biased.

I believe if you powered up the controls with 12v, and spun the encoder/ motor by hand, an ohmmeter could be used accross the phases and battery ground to show a decrease in resistance when the thing switch on. I am guessing you already checked that you were getting switched voltages on any pair of motor leads. This is where a scope would be handy, but I have done it with a analog simpson set to whatever the battery pack max is.