TPS2412 - Power Supply Or Circuit (lower Vout than expected)

Scott,
The TPS2412, as regulation mode controller, will be in a linear regulation mode as long (Rdson * I) < 10mv. That is, anywhere under 10A load with the 1mohm FET will put the IC into this regulation mode. Stability will be affected by the output bulk cap that isn's shown. It needs to be a low esr capacitor, but I suspect you have that already on another page. You also have a Vdd cap and BYP cap so that is good. Is there any active or passive load sharing between the power supplies? Droop sharing?
I suspect the load is so light here, as far as the 3mv reverse current sensing is concerned, that the supplies are going into and out of that mode (sharp Vgate drop) so it would be a good idea to try adding Rset back into this. I would start with a 149k resistor that will set the reverse detect near 0v. 100k will put -1.5mv setting. You can go lower value to test this out. But you need to be careful to note that you will see reverse current over the tolerance band that may or may not be acceptable in the end. The TPS2413, being hysteretic mode, will chatter at light loads so it would be desireable for Iout to be above that level by adjusting Rset likewise, but probably needs to be several mv negative setting to avoid this chatter. The linear mode control is generally better performing at light load, but when in regulation, it will have a higher impedance that can affect transient performance. I was wondering if any active load sharing was affecting the linear operation in the light load area, or contributing.
Try to keep ~ 50mA min load on this as another stability measure. I would play with Rset 1st and then a min load.
Brian