I've read the App Note you giveA while back I had a similar problem and it turned out to be ringing due to trace inductance would drive the VS pin so far negative that it would destroy the high side driver chip. Here is an app note that explains it and the fix. See section 2.4, 4.4 and figure 18.
I saw that in fig.18 there is a schotky diode add between Vs and Gnd, and Rgate between Vs and Vout. Did you use it to prevent negative spike, and is it works?
The explanation in app note is too short for me to understand. I'm a bit confused for the function of those component. Sorry