What I've learned.
When a (3rd partly only?) software instrument is on a track in a summing stack, and you click Learn in the top portion of the of the smart controls Inspector, you can move a parameter on your virtual instrument and map it to a smart control.
However, when you click Learn in the bottom box of the Smart controls Inspector, and twist a knob on your physical controller, you will be inadvertently mapping a function of one of the plugins on your Summing stack track.
Instead of clicking Learn in the top smart controls inspector box, you can click the little "disclosure triangle" in the Parameter Mapping section, then scroll down to the track on which the plugin you wish to automate is instantiated, find said plugin, then find the parameter and select it.
Now, two f%&ked up things happen: 1) the control does map properly to your physical controller, but the smart controls window shows a different parameter moving than the actual one that is mapped( it shows something moving from one of the plugins on the the summing track).
2) When you try automate using the knob on your physical controller, it does not work to record automation! Even though you see it moving the parameter on the plugin, and see the parameter's automation line moving up and down in the background of the automation lane, it will not actually record automation. But, If you use your mouse to grab the same parameter on the plugin, then it does record automation.
Might have to just stop using track stacks and make old school summing busses instead.