There could be several reasons for this. You have not posted any measurement results (oscillograms with galvanically separated oscilloscope), but first of all it looks as if the VIPER16 goes into thermal shutdown and restarts after cooling down. Because at 350V DC you are already quite far at the upper limit of the maximum output power, this could be due to the layout, the buck coil, the free-wheeling diode, etc.
What parameters does the coil have other than the 3.3mH mentioned (saturation current, ohmic resistance)?