The Engine Idle Temperature Management System, or EITMS, is the system you're talking about, not the electronic throttle (tbw). And just rolling the throttle grip forward doesn't cause the EITMS to engage whenever you do so. Rolling the throttle grip forward at idle with the bike sitting still, and holding it until the cruise light flashes either red or green, is how you turn the automatic system on or off. But it doesn't actually shut the rear cylinder down until all the parameters are met, which include engine temps over 287°F if I remember correctly, throttle at idle, bike sitting still, etc. If you are rolling the throttle forward thinking it will instantly cut off the rear cylinder, that's only going to be true if the ECM gets all the proper inputs saying the system should be engaged, and of course if the automatic system is turned on. If the engine temp is below the threshold, twisting that grip all you want won't cause the rear cylinder to shut down. If your attempts at tuning have richened up the mixture enough to suppress engine temps, that can explain why the EITMS kicked in often previously but not so much now. Check your owner's manual for exactly how the EITMS works and how to enable it or disable it. I think you will find what I've said above is true.
It sounds like you need to do some diagnostics first and then get the tune dialed in. You may have a problem related to the Power Commander itself. Funny how those "Auto Tune" products aren't so automatic. Disconnect the PCV and see how the bike runs with just the regular ECM.
Jerry