I feel like an idiot.
I've been using the DR-2d for a while now and almost always run 4ch. I've been opening 4 separate CD Wave windows for the separate sources, the 16 bit matrix and the 24 bit matrix, "stacking" them on top of each other, and doing the tracking separately.
This is kind of like the time I had been manually doing track splits in Audacity because I didn't realize CD Wave did 24 bit...