I don't believe there are separate park/in-gear idle rpm settings in a 7747 ECM. It uses a single table.

There is a %TPS to enable open loop idle setting. Having the %TPS with the throttle closed above this setting could be keeping the ECM out of closed loop idle control. There is also a speed setting that works the same way but I would have to believe the VSS you're using wouldn't give any speed pulses when you are stopped.

Why does your scanner change the idle rpm? Check what it does when connected. There is a resistor you can connect across a couple of ALDL pins to put the ECM into different troubleshooting modes but that resistor is not needed or desired for a 7747 ECM.

You really need to check that the engine is in closed loop idle control or not. you can even try adjusting the idle screw a small amount. The ECM should compensate by adjusting the IAC motor the opposite way to maintain idle. This works as long as you're within the operating range of the IAC motor.