It appears that the charge current is approx 1/10 of the design value. Is it stuck in precharge mode? I know that the loop is closed because I can change the input voltage and watch the duty cycle change. It will also charge the 3s1 battery to 12.6V and turn off. The waveforms look clean, nothing is overheating, all of the voltages appear correct around the IC.
Here is the schematic.