Success!
Kind of. The issue may have been a case of pilot error, I have my gear in a server rack and use a patch bay, and I may have routed the output of the M jack to the bottom row of the patch bay when I wanted the top.
But now I may have another issue.
I'm running the DS-5R in stereo. Using the front outputs to drive the F-2B (Bass to A, Treble to B).
Pickup selector is on the bridge pickup. My expectation is that only channel B will be driven, but both channels are. I get the same behavior if the pickup selector is set to the neck pickup.
Note that I believe the signal coming out of the bass is fine, because with the pickup selector on the bridge pickup, the neck pickup volume as no effect, and visa-versa.
I think I'll go read the FAQ on the F-2B.