Hello Anthony,
I agree it looks like the transistor circuit is not holding the SS pin below 100 mV until VDD reaches the threshold like it should. Perhaps this is because the transistor circuit is power up by +VIN in the schematic? +VIN is essentially the same thing as VDD though an inductor.
The transistor circuit switches high when VDD is at about 26 VDC. I just found that if I slowly vary the VDD voltage around 26 VDC in the range of about 24 VDC - 28 VDC that I can pretty easily enter and get stuck in the hiccup mode. I found the only way out of this is to decrease the voltage and transition high somewhat quickly.
In the first waveform mentioned above without the transistor circuit the 0.1 uF capacitor is not connected to the SS pin.
David Robinson