I had some time to further investigate, and here's what I found out.

So the DISBL# pin on the Renesas is directly connected to GDL1 (pin 24, gate drive output #1) on the SC2446. Probing around the other pins of the SC2446, I can see that COMP1 (pin 5, marked with red in the picture) does the following:

The adjacent SC2446's show a steady 2.6V and 3.0V on COMP1.
On behalf of COMP1 the datasheet says "The Error Amplifier Output for Step-down Controller 1. This pin is used for loop compensation." From the block diagram it looks like the only inputs for the Error Amplifier opamp (EA1) comes from the "Soft-Start And Overload Hiccup Control" module. Reference voltage (REF) is steady 0.5V, and AVCC for the IC measures OK (12V) as well.

I'm now looking at the inputs of the soft-start and OL hiccup control block, and what I don't quite understand is why I'm getting a different reading on SS1/EN1 with my DMM (Fluke 189) and my scope (Siglent SDS 1102CML). Scope shows 1.5V for SS1/EN1 on each SC2446, while a DMM reads 1.9V on the one that's acting up, and 4.2V on the other two.