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I'm also experiencing this.
I suspect it only affects session plugins that set to load on VAM startup
A workaround is to click on 'Return To Scene View' which then allows you to see the full message.
Have an not yet allowed plugin in your "Session Plugins". Set this plugin setup as your default preset. (Having it in your default scene probably works as well)
Enable User Preferences => Misc => "On Startup Skip Top Menu and Load Default Scene"
Restart VaM in Desktop Mode.
Dialog appears partly off screen. You might not even see it, if you happen to look down or up.
Dialog aligns correctly if you open the UI, e.g. by pressing U: