Since your In Command system is the NCS35 here is a link that is worth reading and keeping...
https://www.in-command.net/wp-conten...ting-Guide.pdf
Also if the Zone for the Furnace has a gateway that the dip switches are not configured correctly then the In command will not be able to turn the furnace on because it doesnt know its in the CANBUS chain
Verify dip switch settings on BOTH AC gateways
Also verify there is a terminating resistor installed on the BCM unit.. refer to the link above to see where on the BCM the terminating resistor is installed.
Without it the CANBUS doesnt know where the EOL ( end of line ) is at and may cause issues
I would also verify the latest firmware is loaded into the BCM and check the floor plan config
The gateway sends the signal from the BCM on to the Control box for its Zone AC unit... Which.. also sends the signal down on the two blue wires to the furnace control board to tell furnace to run or not..