Please answer the following questions:
The cables don't matter - I've used two different pairs... and each time the whine disappears if the B-1 output is switched from the ripper to something else, even though the ripper is still physically connected. The effect is the same whether the buffer is powered or not.
Do you have proper ground connection of power supply for computer, Ripper and buffer?
Can you point to the schemes of the buffers you use?
Shielding has no effect, so it's coming in through a cable somewhere..
No way. You've mentioned that even if the Ripper is physically connected to the buffer, but the buffer switched to the other output, the whine disappear. So the cable is not the problem point. I insist that you should try to connect something battery-powered instead of a buffer. Just to eliminate ground loops through the power connector, or no ground on the power connector.
To tell the truth I think it's coming from the computer, that is, being connected to the buffer circuitry allows it to act as a receiver for noise from the computer.
It is possible if the buffer is powered on. But you have the noise regardless of the power. Then it should be inside buffer or inside Ripper.
I think you should try to disconnect all cables and record no signal. If you have the noise in the silence then you have problem with the Ripper.
How would I check the PS capacitors? What would I look for?
It is possible that there is some leakage of the digital frequencies to the input of the ADC. You should check all those filter capacitors for proper grounding (soldering problems?) all power voltages. And the grounding of the chassis too. Maybe you should check for gound loops with ADC input connectors.