This seems like the important part to know. The problem is undoubtedly not Motion Lighting--as both of you acknowledge--if it's turning off the virtual switches, so it's probably something with your virtual-to-"real" switch automation. The above doesn't really make it clear how you're doing that (Groups and Scenes doesn't have any built-in way that I can think of).
Have you considered using the Mirror/Mirror Me app, which was introduced a few firmware versions ago, to "sync" your virtual switches to the real ones? This app was made for another purpose (devices like the RGB Genie remotes and Lutron Aurora that implement level and whatnot capabilities normally associated with real dimmers/bulbs), but it should work. You could probably also just use Groups and Scenes itself and create a "group," even if it contains only one bulb, and then use that group anywhere instead of your virtual devices. You can switch out the "real" devices within that group as needed. Now that I write it out, that sounds like a much better idea...
