This is an interesting finding, @Adam but it seems like it’s more a question for the EnergyPlus gurus and developers. It seems possible that the roof vegetation material isn’t affected by the E+ shadow calculation. Or maybe this issue is that you only included the vegetation layer and did not include a soil layer below it.
If the soil layer doesn’t fix it, it’s worth taking read through the description of the material in the EnergyPlus Input/Output reference:
And if that doesn’t yield any explanations, you should post the question to unmethours where the E+ gurus and developers are: