Dan,
Please look at the updated layout's matrix of examples. It demonstrates that the problem occurs based on the position of "L" (and maybe "V") in the sysex string—not how the channel was set.
FWIW: Each control uses the same channel (02d/01h), set by different means in each column (left: channel changer, middle: design mode, right: hard-coded into the sysex string without using "L"). Consequently, all pickers in the same row send identical sysex messages from the same ticks.
Using a MIDI loopback, changing the value of any picker should cause the other two in its row to change to the same value. But that's not always what happens, and the only difference between each row is the position of L and V in the sysex string's format.
With this format, all controls respond correctly to incoming MIDI:
[F0] 22 22 L 22 V [F7]
With these formats, controls with "L" in their sysex string fail to respond:
[F0] 22 22 22 22 L V [F7]
[F0] 22 22 22 22 V L [F7]
[F0] 22 22 22 V 22 L [F7]
With all these formats, controls with hard-coded channels (and no "L") respond correctly.
You'd mentioned that a directional control shouldn't be affected just because it has an L in it, so this really looks like a bug.