Hello! Always great when a developer is willing to come out and help try to resolve some issues! We definitely appreciate the help. I, for one, love Stella. I continue to use it, but I do see this problem as a nuisance for us Mala users
Just a small description of what Mala is. It's what we call a "front end" program. We here at this site make arcade machines, and most of us use multiple emulators on them. Mala is a program that links all these emulators together. It acts as a launch screen. It can show screen shots, video previews, box art, or anything you want for all of the games. So on my machine, Stella is just one of many emulators that I have set up to work in Mala.
If you're at all curious to see it in operation, you can check the few videos below of my arcade machines.
There's no Stella footage in my videos, but it can show you the general idea of what Mala does anyway...
Now Mala was first and foremost designed to work with MAME. Which is the emulator for arcade games. So you will not actually be able to use Mala without having Mame installed on your machine. But not to worry, its very easy to set up. I've wrote up some quick instructions for you and attached them. The instructions should show you how to install Mala, then Mame, and then configure Mala to work with Stella. In that document it also shows you the settings, for me at least, that make this "screen shift" issue occur. I cannot speak for others who have this problem, but I would assume that their settings and circumstances are pretty similar to my own. Sorry the instructions are not totally polished, but they should be good enough to get you going I think. Please let me know if you have any questions, or need me to do any testing on my side! Otherwise, let us know what you find out. My ultimate goal is to get Stella to run as large as possible on my screen, and then upon exit, have my Mala menu still in tact. However, my work around right now works, but the size in which it's emulated on the screen is greatly decreased.