Another update. It is definitely the custom schemes that have the problem. Clearly, this is a bug in the version I'm using (13.0.2). The problem is due to the custom scheme being saved with a "Zinger" property. If I take the following lines out of the XML file and re-load the Personality settings, the LEDs start working again:
<state id="e_LEDState_Zinger">
<hue>0</hue><sat>0</sat><lum>0</lum>
</state>
I figure that the hue, saturation, and luminosity being set to 0 doesn't help. None of the built-in schemes have this property, so taking it out isn't an issue. Doing so makes it work!
I'll upgrade the Carbonite and see if it still happens with 13.0.4 and report back.
UPDATE: The problem still exists in 13.0.4. Creating a new custom scheme disables the LEDs on the fader bars,
#Carbonite