Here's an interesting graph:
It shows what my speed-mode Jaguars are reporting as their % voltage output, every 20ms.
This corresponds to what I see my secondary motors doing.
The important part here is that the speed mode Jaguars are, in actuality, driving the motors at a constant speed (approximately half of full-speed).
This leads me to believe there is an issue with how Jaguars report their output when they are in internal closed-loop control. They may be reporting what they are doing instantaneously, but that is not a useful value at 50hz.
If this is not remedied, my only option is to wire the quadrature encoder channels to both Jaguars.