Why won't my furnace run on the generator?

I have a portable generator for my standby power connected to a sub panel through a manual transfer switch supplied by a breaker in the main panel. I have separated the neutral and the ground at the sub panel and the transfer switch–they are only bound at the main panel. The problem I’m having is the furnace will not operate on the generator but works fine on normal power.

The furnace model is a GOODMAN GMVC950905DXAB. The generator is a GENERAC XG8000. The thermostat is a Honeywell RTH5160 which uses batter power and only one 15AMP circuit to the furnace, which measures 115.7 volts.

There is a circuit board on the furnace with a 2 digit readout on it that puts out an 88 code that has no definition on the troubleshooting area, but there are two LEDs at the top of the circuit board. One is marked RX and the other is marked status. The RX blinks on generator power but not on normal power. The status LED blinks ounce and then goes out. Normal operation then OP comes on in the readout and the furnace starts to run.