Ain’t Automap great!
Unfortunately, the disappearing VST guis and other such is a function of how Steinberg has incorporated Windows’ windows. You’ll find loads of similar complaints if you search through the forum archives.
The good news is that once you have your Automap templates set up and only need to use automap and not assign parameters to the controls, the Automap gui will sit nicely on top of Cubase ‘in focus’ with all necessary or desired open windows … and you can use the ‘View’ button on your Automap controller to hide or show the Automap gui. Just don’t touch that screen with your mouse!
I understand there has been a significant improvement in how another Steinberg product, WaveLab, displays it’s windows, and many suspect this is a major improvement (along with being able to maximize windows without having to resize them or lose things off the visible area of the window) that will arrive in the not too distant future.
I should add that in the past when I’ve wanted to design an Automap template for a complicated VST or VSTi with lots of parameters, I’ve opened the VST/ VSTi in a simple program like Toby’s Minihost or Chainer … where I don’t lose sight of the GUI while setting up Automap.