Interesting...
I just did new build from scratch for the billionth time, starting all the way from making new RPG Maker project to get latest update files. Including downloading the latest versions of plugins.
Now, when I install the package, on first run, the plugins work. Then when I close the app and re-open, no plugins run. It will only run the plugins on the first run of the app.
So if I uninstall and re-install, I can run the app with plugins working. Does this behavior make any sense to anyone? Note, this is when installing the x86 version of the UWP app. When running the ARM version the plugins just don't work at all.
Also, I tried building as an Ionic app which made no difference. So in all I've tried building it as UWP with WinJS, Cordova, and Ionic. All failed to handle running plugins. It always works in debugging though.