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Yep, seems to be an unfortunate combination of Gnome Shell's latest versions being a bit overzealous with this popup (I get the same for almost every heavier application I start), and Unity's splash screen feature.  If it stays as an issue in the long run we can always just ditch Unity's splash screen stuff and build out own, but for now I'd actually wait and see if Gnome gets it back to a bit better balance again...