Akshay,
Thanks for the response and I apologize for my delay. The input to the supply is 3.3V regulated. The output voltage is 12 volts up to 400mA max. My switching frequency is supposed to be around 158kHz and the frequency modulation is f/16.
We have used this boost in several other similar applications and have not had the same issue. This particular iteration was done years ago and was assumed to be okay, but my initial thought matched yours in regards to the instability.
Below are two scope traces, one signal is the gate drive (green), and the other is the gate of the FET connected to the FA pin. One capture is a single shot, the other shows infinite persistence.
I will e-mail the schematic directly as I'd rather not publish it on a public forum.
Thanks,
--Jim