I don’t know what Indigo supports regarding using links with Indigo. That configuration does work with the ISY device. Using the Broadcast Status Chg option does raise the possibility that when the Enable Analog Inputs option was set the Broadcast Status Chg option was reset. The full Configuration Register is set when any option is set so it is necessary for Indigo to set all the options that are desired when any one option is changed.
I will set up a test using the Broadcast Status Chg configuration and see if I can reproduce what you are seeing.