Why is SMPS controller IC failing?
I have a suspicion that your problem might have to do with the bootstrap circuit, as detailed in section 5.3 of the data sheet. Some evidence leads to this conclusion:


You are likeley using larger MOSFETs than in the original design (because your overall power is greater), thus you are dealing with a higher gate charge, resulting in a higher current that must be delivered by the integrated bootstrap circuit. It could be that the bootstrap circuit dissipates more power than it was designed for and fails, sometimes resulting in a bad output driver for the high side MOSFET, sometimes taking the MOSFET with it. Adding an external, fast and high-voltage bootstrap diode might help. Note that the calculation in Eq. 9 of sect. 5.3 uses the typical on-resistance of the integrated bootstrap circuit. It's a better idea to use the max. value from table 4 which is twice as high.
Once the circuit goes into overload, you say that the frequency drops. During these prolonged on-times, the voltage across the external bootstrap capacitor might become too low to keep the high side MOSFET saturated, causing it to have a higher on-resistance, excessive losses and thermal overstress. However, in this case, it would be the high-side MOSFET that fails first. Check the voltage across the bootstrap capacitor. A bigger capacitor might help, but this will likely put more stress on the integrated bootstrap driver or the external diode that might be necessary anyway.


Another possibility could be that you are exceeding the maximum slew rates for the high-side driver. This might cause it to do weird things.

Concerning the negative spikes, an external protective clamping diode at each driver's output might help (K=Vout,HS; A=GND,LS and K=Vout,HS; A=GND,HS). Something as simple as a 1N4148 might be enough.